============================================================ | | | Crystallography & NMR System (CNS) | | CNSsolve | | | ============================================================ Version: 1.1 Status: General release ============================================================ Written by: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren. Copyright (c) 1997-2001 Yale University ============================================================ Running on machine: mark-a-depristos-power-mac-g5.lo (Unix-g77,32-bit) Program started by: mdepristo Program started at: 09:31:21 on 15-Sep-2005 ============================================================ FFT3C: Using FFTPACK4.1 CNSsolve>{- begin block parameter definition -} define( DEFINE>{===>} high_res=2.300000; DEFINE>{===>} structure_infile="refine-0-1.mtf"; DEFINE>{===>} coordinate_infile_1="refine-0-2_mtf.pdb"; DEFINE>{===>} reflection_infile_1="9ilb.hkl"; DEFINE>{===>} output_root="refine-0-2"; DEFINE>{===>} sg="P4(3)"; DEFINE>{* unit cell parameters in Angstroms and degrees *} DEFINE>{+ table: rows=1 "cell" cols=6 "a" "b" "c" "alpha" "beta" "gamma" +} DEFINE>{===>} a=55.02; DEFINE>{===>} b=55.02; DEFINE>{===>} c=77.16; DEFINE>{===>} alpha=90.00; DEFINE>{===>} beta=90.00; DEFINE>{===>} gamma=90.00; DEFINE>{===>} high_res= 2.30; DEFINE> DEFINE>{======================= molecular structure =========================} DEFINE> DEFINE>{* parameter files *} DEFINE>{===>} parameter_infile_1="CNS_TOPPAR:protein_rep.param"; DEFINE>{===>} parameter_infile_2="CNS_TOPPAR:dna-rna_rep.param"; DEFINE>{===>} parameter_infile_3="CNS_TOPPAR:water_rep.param"; DEFINE>{===>} parameter_infile_4="CNS_TOPPAR:ion.param"; DEFINE>{===>} parameter_infile_5="CNS_TOPPAR:carbohydrate.param"; DEFINE> DEFINE>{* topology files *} DEFINE>{===>} topology_infile_1="CNS_TOPPAR:protein.top"; DEFINE>{===>} topology_infile_2="CNS_TOPPAR:dna-rna.top"; DEFINE>{===>} topology_infile_3="CNS_TOPPAR:water.top"; DEFINE>{===>} topology_infile_4="CNS_TOPPAR:ion.top"; DEFINE>{===>} topology_infile_5="CNS_TOPPAR:carbohydrate.top"; DEFINE> DEFINE>{====================== crystallographic data ========================} DEFINE> DEFINE>{* anomalous f' f'' library file *} DEFINE>{* If a file is not specified, no anomalous contribution will be included *} DEFINE>{+ choice: "CNS_XRAYLIB:anom_cu.lib" "CNS_XRAYLIB:anom_mo.lib" "" user_file +} DEFINE>{===>} anom_library=""; DEFINE> DEFINE>{* reciprocal space array containing observed amplitudes: required *} DEFINE>{===>} obs_f="fobs"; DEFINE> DEFINE>{* reciprocal space array containing sigma values for amplitudes: required *} DEFINE>{===>} obs_sigf="sigma"; DEFINE> DEFINE>{* reciprocal space array containing test set for cross-validation: required *} DEFINE>{* cross-validation should always be used, with the possible exception DEFINE> of a final round of refinement including all data *} DEFINE>{* cross-validation is always required for the maximum likelihood targets *} DEFINE>{===>} test_set="test"; DEFINE> DEFINE>{* number for selection of test reflections: required for cross-validation *} DEFINE>{* ie. reflections with the test set array equal to this number will be DEFINE> used for cross-validation, all other reflections form the working set *} DEFINE>{===>} test_flag=0; DEFINE> DEFINE>{* reciprocal space array containing weighting scheme for observed DEFINE> amplitudes: optional *} DEFINE>{* only used for the "residual" and "vector" targets - this will DEFINE> default to a constant value of 1 if array is not present *} DEFINE>{===>} obs_w=""; DEFINE> DEFINE>{* reciprocal space array containing observed intensities: optional *} DEFINE>{* required for the "mli" target *} DEFINE>{===>} obs_i=""; DEFINE> DEFINE>{* reciprocal space array containing sigma values for intensities: optional *} DEFINE>{* required for the "mli" target *} DEFINE>{===>} obs_sigi=""; DEFINE> DEFINE>{* reciprocal space arrays with experimental phase probability DEFINE> distribution: optional *} DEFINE>{* Hendrickson-Lattman coefficients A,B,C,D *} DEFINE>{* required for the "mlhl" target *} DEFINE>{+ table: rows=1 "HL coefficients" cols=4 "A" "B" "C" "D" +} DEFINE>{===>} obs_pa=""; DEFINE>{===>} obs_pb=""; DEFINE>{===>} obs_pc=""; DEFINE>{===>} obs_pd=""; DEFINE> DEFINE>{* complex reciprocal space array containing experimental phases: optional *} DEFINE>{* required for the "mixed" and "vector" targets *} DEFINE>{===>} obs_phase=""; DEFINE> DEFINE>{* reciprocal space array containing experimental figures of merit: optional *} DEFINE>{* required for the "mixed" target *} DEFINE>{===>} obs_fom=""; DEFINE> DEFINE>{* resolution limits for data included in map calculation *} DEFINE>{* all data available should be included in the map calculation *} DEFINE>{+ table: rows=1 "resolution" cols=2 "lowest" "highest" +} DEFINE>{===>} low_res=500.0; DEFINE> DEFINE>{* apply rejection criteria to amplitudes or intensities *} DEFINE>{+ choice: "amplitude" "intensity" +} DEFINE>{===>} obs_type="amplitude"; DEFINE> DEFINE>{* Observed data cutoff criteria: applied to amplitudes or intensities *} DEFINE>{* reflections with magnitude(Obs)/sigma < cutoff are rejected. *} DEFINE>{===>} sigma_cut=0.0; DEFINE> DEFINE>{* rms outlier cutoff: applied to amplitudes or intensities *} DEFINE>{* reflections with magnitude(Obs) > cutoff*rms(Obs) will be rejected *} DEFINE>{===>} obs_rms=10000; DEFINE> DEFINE>{=================== non-crystallographic symmetry ===================} DEFINE> DEFINE>{* NCS-restraints/constraints file *} DEFINE>{* see auxiliary/ncs.def *} DEFINE>{===>} ncs_infile=""; DEFINE> DEFINE>{============ initial B-factor and bulk solvent corrections ==========} DEFINE> DEFINE>{* initial B-factor correction *} DEFINE>{+ choice: "no" "isotropic" "anisotropic" "anisotropic_fixed_isotropic" +} DEFINE>{===>} bscale="anisotropic"; DEFINE> DEFINE>{* lower resolution limit for B-factor correction *} DEFINE>{* the correction can only be calculated using data truncated at a DEFINE> lower resolution limit of between 8 and 6 A. The correction will be DEFINE> applied to all reflections *} DEFINE>{===>} low_res_bscale=6.0; DEFINE> DEFINE>{* bulk solvent correction *} DEFINE>{* a mask is required around the molecule(s). The region DEFINE> outside this mask is the solvent region *} DEFINE>{+ choice: true false +} DEFINE>{===>} bulk_sol=true; DEFINE> DEFINE>{* bulk solvent mask file *} DEFINE>{* mask will be read from O type mask file if a name is given DEFINE> otherwise calculated from coordinates of selected atoms *} DEFINE>{===>} bulk_mask_infile=""; DEFINE> DEFINE>{* solvent density level *} DEFINE>{* if negative, determined automatically DEFINE> if positive, fixed at value given *} DEFINE>{===>} sol_k=-1; DEFINE> DEFINE>{* solvent B-factor *} DEFINE>{* if negative, determined automatically DEFINE> if positive, fixed at value given *} DEFINE>{===>} sol_b=-1; DEFINE> DEFINE>{========================== atom selection ===========================} DEFINE> DEFINE>{* select atoms to be included in map calculation *} DEFINE>{* this should include all conformations if multiple conformations are used *} DEFINE>{===>} atom_select=(known and not hydrogen); DEFINE> DEFINE>{* select fixed atoms *} DEFINE>{* note: isolated atoms and atoms are diatomic molecules are automatically DEFINE> fixed during torsion angle dynamics, and atoms at special positions are DEFINE> automatically fixed for all types of dynamics. So, you don't have to DEFINE> explicitly fix them here. *} DEFINE>{===>} atom_fixed=(none); DEFINE> DEFINE>{* select atoms to be treated as rigid groups during torsion angle dynamics *} DEFINE>{===>} atom_rigid=(none); DEFINE> DEFINE>{* select atoms to be omitted from map calculation *} DEFINE>{===>} atom_omit=(none); DEFINE> DEFINE>{* size of the neighborhood that is also omitted *} DEFINE>{===>} sphere=3.5; DEFINE> DEFINE>{* size of the surrounding harmonically restrained cushion *} DEFINE>{===>} cushion=2; DEFINE> DEFINE>{* select atoms to be harmonically restrained during annealing *} DEFINE>{===>} atom_harm=(none); DEFINE> DEFINE>{* harmonic restraint constant - for harmonically restrained atoms *} DEFINE>{===>} k_harmonic=10; DEFINE> DEFINE>{* select atoms in alternate conformation 1 *} DEFINE>{===>} conf_1=(none); DEFINE> DEFINE>{* select atoms in alternate conformation 2 *} DEFINE>{===>} conf_2=(none); DEFINE> DEFINE>{* select atoms in alternate conformation 3 *} DEFINE>{===>} conf_3=(none); DEFINE> DEFINE>{* select atoms in alternate conformation 4 *} DEFINE>{===>} conf_4=(none); DEFINE> DEFINE>{* additional restraints file *} DEFINE>{* eg. auxiliary/dna-rna_restraints.def *} DEFINE>{===>} restraints_infile=""; DEFINE> DEFINE>{==================== map generation parameters ======================} DEFINE> DEFINE>{* maps are calculated u*Fo - v*Fc *} DEFINE>{* eg. 2fo-fc map -> u=2 and v=1 *} DEFINE> DEFINE>{* specify u *} DEFINE>{===>} u=2; DEFINE> DEFINE>{* specify v *} DEFINE>{===>} v=1; DEFINE> DEFINE>{* type of map *} DEFINE>{+ list: sigmaa: (u m|Fo| - v D|Fc|)^exp(i phi_calc) DEFINE> m and D calculated from sigmaa DEFINE> unweighted: (u |Fo| - v k|Fc|)^exp(i phi_calc) DEFINE> no figure-of-merit weighting DEFINE> combined: (u m|Fo|^exp(i phi_comb) - v D|Fc|^exp(i phi_calc)) DEFINE> model and experimental phases combined, m and D from sigmaa DEFINE> observed: (u m|Fo|^exp(i phi_obs) - v k m|Fc|^exp(i phi_calc)) DEFINE> observed phases and fom from phase probability distribution DEFINE> gradient: d(target)/dFc DEFINE> gradient of the current crystallographic target wrt Fc DEFINE> NB. experimental phases must be supplied as a phase DEFINE> probability distribution in the Hendrickson-Lattman arrays +} DEFINE>{+ choice: "sigmaa" "unweighted" "combined" "observed" "gradient" +} DEFINE>{===>} map_type="sigmaa"; DEFINE> DEFINE>{* use model amplitudes for unmeasured data *} DEFINE>{* this will not be applied to gradient or difference maps *} DEFINE>{+ choice: true false +} DEFINE>{===>} fill_in=false; DEFINE> DEFINE>{* scale map by dividing by the rms sigma of the map *} DEFINE>{* otherwise map will be on an absolute fobs scale *} DEFINE>{+ choice: true false +} DEFINE>{===>} map_scale=true; DEFINE> DEFINE>{* map format *} DEFINE>{* choice: "cns" "ezd" *} DEFINE>{===>} map_format="cns"; DEFINE> DEFINE>{* map grid size: dmin*grid *} DEFINE>{* use grid=0.25 for better map appearance *} DEFINE>{===>} grid=0.25; DEFINE> DEFINE>{* extent of map *} DEFINE>{+ choice: "molecule" "asymmetric" "unit" "box" "fract" +} DEFINE>{===>} map_mode="molecule"; DEFINE> DEFINE>{* select atoms around which map will be written *} DEFINE>{* change if different to atoms selected for map calculation *} DEFINE>{===>} atom_map=(known and not hydrogen); DEFINE> DEFINE>{* cushion (in Angstroms) around selected atoms in "molecule" mode *} DEFINE>{===>} map_cushion=3.0; DEFINE> DEFINE>{* limits in orthogonal angstroms for box mode or DEFINE> fractional coordinates for fract mode *} DEFINE>{+ table: rows=3 "x" "y" "z" cols=2 "minimum" "maximum" +} DEFINE>{===>} xmin=0.; DEFINE>{===>} xmax=0.; DEFINE>{===>} ymin=0.; DEFINE>{===>} ymax=0.; DEFINE>{===>} zmin=0.; DEFINE>{===>} zmax=0.; DEFINE> DEFINE>{======================= annealing parameters ========================} DEFINE> DEFINE>{* carry out annealing *} DEFINE>{+ choice: true false +} DEFINE>{===>} anneal=true; DEFINE> DEFINE>{* type of molecular dynamics *} DEFINE>{* it is possible that torsion angle dynamics may encounter a problem DEFINE> with the molecular topology after certain parts of the structure have DEFINE> been omitted. If this happens the program will terminate with an DEFINE> error and cartesian dynamics must be used instead *} DEFINE>{+ choice: "torsion" "cartesian" +} DEFINE>{===>} md_type="torsion"; DEFINE> DEFINE>{* starting temperature *} DEFINE>{===>} temperature=1000; DEFINE> DEFINE>{* drop in temperature (K) per set of dynamics *} DEFINE>{===>} cool_rate=25; DEFINE> DEFINE>{* seed for random number generator *} DEFINE>{* change to get different initial velocities *} DEFINE>{===>} seed=82364; DEFINE> DEFINE>{* torsion-angle MD parameters *} DEFINE>{* increase these values if the program terminates with the message DEFINE> that one of these parameters is exceeded *} DEFINE> DEFINE>{* maximum unbranched chain length *} DEFINE>{* increase for long stretches of polyalanine *} DEFINE>{===>} torsion_maxlength=50; DEFINE>{* maximum number of distinct bodies *} DEFINE>{===>} torsion_maxtree=20; DEFINE>{* maximum number of chains (increase for large molecules) *} DEFINE>{===>} torsion_maxchain=1000; DEFINE>{* maximum number of bonds to an atom *} DEFINE>{===>} torsion_maxbond=6; DEFINE> DEFINE>{======================= minimization parameters ======================} DEFINE> DEFINE>{* final steps of conjugate gradient minimization *} DEFINE>{===>} mini_steps=100; DEFINE> DEFINE>{======================= refinement parameters ========================} DEFINE> DEFINE>{* refinement target *} DEFINE>{+ list: mlf: maximum likelihood target using amplitudes DEFINE> mli: maximum likelihood target using intensities DEFINE> mlhl: maximum likelihood target using amplitudes DEFINE> and phase probability distribution DEFINE> residual: standard crystallographic residual DEFINE> vector: vector residual DEFINE> mixed: (1-fom)*residual + fom*vector DEFINE> e2e2: correlation coefficient using normalized E^2 DEFINE> e1e1: correlation coefficient using normalized E DEFINE> f2f2: correlation coefficient using F^2 DEFINE> f1f1: correlation coefficient using F +} DEFINE>{+ choice: "mlf" "mli" "mlhl" "residual" "vector" "mixed" DEFINE> "e2e2" "e1e1" "f2f2" "f1f1" +} DEFINE>{===>} reftarget="mlf"; DEFINE> DEFINE>{* number of bins for refinement target *} DEFINE>{* this will be determined automatically if a negative value is given DEFINE> otherwise the specified number of bins will be used *} DEFINE>{===>} target_bins=-1; DEFINE> DEFINE>{* lower resolution limit for refinement *} DEFINE>{* the full resolution range of observed data should be used in refinement. DEFINE> A bulk solvent correction should be applied to allow the use of low DEFINE> resolution terms. If no bulk solvent correction is applied, data must DEFINE> be truncated at a lower resolution limit of between 8 and 6 Angstrom. *} DEFINE>{===>} refine_low_res=500.0; DEFINE> DEFINE>{* Wa weight for X-ray term *} DEFINE>{* this will be determined automatically if a negative value is given. DEFINE> Note: wa can be very different depending on the target - if it is not DEFINE> determined automatically make sure an appropriate value is used *} DEFINE>{===>} wa=-1; DEFINE> DEFINE>{* memory allocation for FFT calculation *} DEFINE>{* this will be determined automatically if a negative value is given DEFINE> otherwise the specified number of words will be allocated *} DEFINE>{===>} fft_memory=-1; DEFINE> DEFINE>{=========================== output files ============================} DEFINE> DEFINE>{* write map file *} DEFINE>{+ choice: true false +} DEFINE>{===>} write_map=true; DEFINE> DEFINE>{* do peak picking on map *} DEFINE>{* optional - use water_pick.inp to pick waters *} DEFINE>{+ choice: true false +} DEFINE>{===>} peak_search=false; DEFINE> DEFINE>{* number of peaks to pick from map *} DEFINE>{===>} peak_num=30; DEFINE> DEFINE>{* write a reflection file with the Fourier coefficients of the map *} DEFINE>{+ list: arrays written: DEFINE> map_fom: FOM weight applied to observed data DEFINE> map_phase: phases used for observed data DEFINE> map_scale: scale factor applied to calculated data DEFINE> map_coeff: Fourier map coefficients - map=ft(map_coeff) +} DEFINE>{+ choice: true false +} DEFINE>{===>} write_coeff=false; DEFINE> DEFINE>{===========================================================================} DEFINE>{ things below this line do not normally need to be changed } DEFINE>{===========================================================================} DEFINE> DEFINE> ) {- end block parameter definition -} CNSsolve> CNSsolve> checkversion 1.1 Program version= 1.1 File version= 1.1 CNSsolve> CNSsolve> evaluate ($log_level=quiet) Assuming literal string "QUIET" EVALUATE: symbol $LOG_LEVEL set to "QUIET" (string) CNSsolve> CNSsolve> structure @&structure_infile end ASSFIL: file refine-0-1.mtf opened. STRUcture>data_cns_mtf REMARKS FILENAME="refine-0-1.mtf" REMARKS DATE:15-Sep-2005 09:31:20 created by user: mdepristo REMARKS VERSION:1.1 Status of internal molecular topology database: -> NATOM= 1275(MAXA= 40000) NBOND= 1242(MAXB= 40000) -> NTHETA= 1672(MAXT= 80000) NGRP= 211(MAXGRP= 40000) -> NPHI= 792(MAXP= 80000) NIMPHI= 499(MAXIMP= 40000) -> NNB= 0(MAXNB= 40000) STRUcture> STRUcture> end CNSsolve> CNSsolve> coordinates @&coordinate_infile_1 ASSFIL: file refine-0-2_mtf.pdb opened. COOR>REMARK FILENAME="refine-0-2_mtf.pdb" COOR>REMARK DATE:15-Sep-2005 09:31:20 created by user: mdepristo COOR>REMARK VERSION:1.1 COOR>ATOM 1 CB ALA A 1 -17.953 16.662 -22.034 1.00 58.44 A COOR>ATOM 2 C ALA A 1 -20.198 17.727 -22.156 1.00 56.81 A CNSsolve> CNSsolve> parameter PARRDR> if ( &BLANK%parameter_infile_1 = false ) then NEXTCD: condition evaluated as true PARRDR> @@¶meter_infile_1 ASSFIL: file /sw/share/xtal/cns_solve_1.1/libraries/toppar/protein_rep.param opened. PARRDR>remarks file toppar/protein_rep.param PARRDR>remarks protein parameters for crystallographic structure determination PARRDR>remarks with "soft" (purely repulsive) van der Waals parameters. PARRDR>remarks PARRDR>remarks file toppar/protein_rep.param PARRDR>remarks Parameter file including bond and angle parameters PARRDR>remarks derived from Cambridge Data Base model structures PARRDR>remarks (R. A. Engh and R. Huber, Acta Cryst. Sect. A., 1991). PARRDR>remarks PARRDR>remarks Nonbonded parameters taken from PROLSQ using REPEL function. PARRDR>remarks Small dihedral angle energy constants set to uniform small value. PARRDR>remarks All other dihedral and improper energy constants set to uniform PARRDR>remarks large values. PARRDR>remarks PARRDR>remarks Warning: these parameters are not suitable for free MD simulations PARRDR>remarks PARRDR> PARRDR>! PARRDR>! References: PARRDR>! Engh, R.A. and Huber, R. (1991). Accurate Bond and PARRDR>! Angle Parameters for X-ray Protein-Structure Refinement, PARRDR>! Acta Cryst. A47, 392-400. PARRDR>! PARRDR>! Hendrickson W.A. and Konnert J.H. in "Computing in PARRDR>! Crystallography" (ed. R. Diamond, S. Ramaseshan PARRDR>! and K. Venkatesan) (Bangalore, Indian Institute of PARRDR>! Science, 1980) 13.01-13.23 PARRDR>! PARRDR> PARRDR>set echo=off message=off end Program version= 1.1 File version= 1.1 PARRDR> end if PARRDR> if ( &BLANK%parameter_infile_2 = false ) then NEXTCD: condition evaluated as true PARRDR> @@¶meter_infile_2 ASSFIL: file /sw/share/xtal/cns_solve_1.1/libraries/toppar/dna-rna_rep.param opened. PARRDR>remarks file toppar/dna-rna_rep.param PARRDR>remarks nucleic acid rna-dna parameter file for crystallographic PARRDR>remarks structure determination using soft (purely repulsive) PARRDR>remarks van der Waals parameters. PARRDR>remarks PARRDR>remarks Warning: these parameters are not suitable for free MD simulations PARRDR>remarks PARRDR> PARRDR>remarks Bases 18.75% Sugar 56.6% Phos 154.8% PARRDR>remarks K= scale*(kT/sigma**2), scales=Base 0.1875, Sugar 0.566, Phos 1.548 PARRDR>remarks Nonbonded parameters taken from PROLSQ using REPEL function PARRDR>remarks Note: use water parameters in protein_rep.param PARRDR> PARRDR>! removed references to CA, CF, CS, MG, NH3, OS (ATB 12/30/94) PARRDR>! removed TIP3 water model (ATB 12/30/94) PARRDR>! mapped NA->NNA, CH3E->CC3E (ATB 12/30/94) PARRDR> PARRDR>! PARRDR>!Please cite the following reference when using these parameters: PARRDR>!G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, PARRDR>! New Parameters for the Refinement of Nucleic Acid Containing Structures, PARRDR>! Acta Cryst. D, 52, 57-64 (1996). PARRDR>! PARRDR>! Oct. 8, 1996 - Modified by Alexey Bochkarev (McMaster University) PARRDR>! to process properly 5PHO (5'-terminus with phosphate) patch. PARRDR>! Geometry and charges of -O5'-PO3 group were taken from PARRDR>! Saenger W. 1984. Principles of Nucleic Acid Structure PARRDR>! All modifications are placed between: PARRDR>!***AB*** PARRDR>!....included fragment PARRDR>!***AB end*** PARRDR>! New atomic types were introduced (see dna-rna.top) to describe PARRDR>! -O5'-PO3 group: O5H (O5') O1PH (O1P) O2PH (O2P) PARRDR>! in addition to existing OH (O5T) PARRDR> PARRDR>set echo=off message=off end Program version= 1.1 File version= 1.1 PARRDR> end if PARRDR> if ( &BLANK%parameter_infile_3 = false ) then NEXTCD: condition evaluated as true PARRDR> @@¶meter_infile_3 ASSFIL: file /sw/share/xtal/cns_solve_1.1/libraries/toppar/water_rep.param opened. PARRDR>remarks file toppar/water.param PARRDR>remarks water parameters for structure determination PARRDR>remarks PARRDR> PARRDR>set echo=false end Program version= 1.1 File version= 1.1 EVALUATE: symbol $VDW_RADIUS_O set to 2.90000 (real) EVALUATE: symbol $VDW_RADIUS_HH set to 1.60000 (real) EVALUATE: symbol $VDW_RADIUS_O set to 2.58361 (real) EVALUATE: symbol $VDW_RADIUS_HH set to 1.42544 (real) EVALUATE: symbol $VDW_RADIUS14_O set to 2.31634 (real) EVALUATE: symbol $VDW_RADIUS14_HH set to 1.15817 (real) EVALUATE: symbol $VDW_EPS set to 0.100000 (real) PARRDR> PARRDR> end if PARRDR> if ( &BLANK%parameter_infile_4 = false ) then NEXTCD: condition evaluated as true PARRDR> @@¶meter_infile_4 ASSFIL: file /sw/share/xtal/cns_solve_1.1/libraries/toppar/ion.param opened. PARRDR>remarks file toppar/ion.param PARRDR>remarks nonbonded parameters for common ions PARRDR>remarks new parameters derived from literature for single atom species PARRDR>remarks PDA 02/09/99 PARRDR> PARRDR>set echo=off end Program version= 1.1 File version= 1.1 PARRDR> end if PARRDR> if ( &BLANK%parameter_infile_5 = false ) then NEXTCD: condition evaluated as true PARRDR> @@¶meter_infile_5 ASSFIL: file /sw/share/xtal/cns_solve_1.1/libraries/toppar/carbohydrate.param opened. PARRDR>remarks file toppar/carbohydrate.param PARRDR>REMARKS Parameter file for pyranose sugars for crystallographic PARRDR>remarks structure determination. PARRDR>remarks PARRDR> PARRDR>REMARKS Bill Weis 10-July-1988 PARRDR>REMARKS Additions for atom type combinations not covered in PARAM19X.PRO. PARRDR>REMARKS Needed additions are for ether oxygen and aliphatic carbon in all-atom PARRDR>REMARKS representation used for sugars (type CC). Ditto for type HA. PARRDR>REMARKS Values from J. Brady glucose parameters unless noted. PARRDR>REMARKS These should be sufficient for refinement. PARRDR> PARRDR>REMARKS Additions 6-March-1992 Bill Weis PARRDR>REMARKS New atom types CCA, CCE, OA for the C1 & O1 positions to account PARRDR>REMARKS for different bond and angle values due to the anomeric effect. PARRDR>REMARKS More accurate equilibrium values for bond angle around this oxygen PARRDR>REMARKS in glycosidic linkages. CCE for equatorial O1, CCA for PARRDR>REMAKRS axial O1. For free sugar, keep OH1 as O1 atomtype; changed to OA PARRDR>REMARKS for linkages. PARRDR>REMARKS References: G.A. Jeffrey (1990) Acta Cryst B46, 89-103; PARRDR>REMARKS K. Hirotsu & A.Shimada, (1974) Bull. Chem. Soc. Japan, 47, 1872-1879. PARRDR> PARRDR>REMARKS This set has been modified to be roughly consistent with PARRDR>REMARKS the csd-derived protein parameters of Engh and Huber. PARRDR>REMARKS New atom type CC6 for exocyclic 6 carbon PARRDR>REMARKS Bill Weis 5/11/92 PARRDR> PARRDR>set echo=false end Program version= 1.1 File version= 1.1 PARRDR> PARRDR> end if PARRDR> end CNSsolve> CNSsolve> xray XRAY> XRAY> @CNS_XTALLIB:spacegroup.lib (sg=&sg;) ASSFIL: file /sw/share/xtal/cns_solve_1.1/libraries/xtal/spacegroup.lib opened. XRAY>! file libraries/xtal/spacegroup.lib XRAY>! library of symmetry operators for CNS XRAY>! Automatically generated with SgInfo Version 2.00a13 XRAY> XRAY>module MODULE-DECLARATION>( MODULE-DECLARATION> &sg=$sg; MODULE-DECLARATION> &sgparam=$sgparam; MODULE-DECLARATION>) &_2_SG set to &_1_SG XRAY> XRAY>set message ? end MESSage=NORM XRAY>evaluate ($message_old=$result) EVALUATE: symbol $MESSAGE_OLD set to "NORM" (string) XRAY>set echo ? end ECHO=TRUE {ON} XRAY>evaluate ($echo_old=$result) EVALUATE: symbol $ECHO_OLD set to TRUE (logical) XRAY>set echo=off message=off end Program version= 1.1 File version= 1.1 SYMMETRY: found symmetry operators for space group "P4(3)" in library XRAY> XRAY> XRAY> a=&a b=&b c=&c alpha=&alpha beta=&beta gamma=&gamma XRAY> XRAY> @CNS_XRAYLIB:scatter.lib ASSFIL: file /sw/share/xtal/cns_solve_1.1/libraries/xray/scatter.lib opened. XRAY>! file libraries/xray/scatter.lib XRAY>! Atomic scattering factors without anomalous contribution XRAY>! Library for CNS XRAY> XRAY>! Authors: Paul Adams, Joe Jaeger, and Axel T. Brunger XRAY> XRAY>!BEWARE: XRAY>!(1) element Cf (Californium) has to be referred to as Cff XRAY>!(2) element Sm (Samarium) has to be referred to as Smm XRAY>!(3) element Np (Neptunium) has to be referred to as Npp XRAY>!(3) types of elements with ionic state (i.e., +/-) specifications have XRAY>! to be put in double quotes in selection statements. XRAY> XRAY>set message ? end MESSage=NORM XRAY>evaluate ($message_old_sclib=$result) EVALUATE: symbol $MESSAGE_OLD_SCLIB set to "NORM" (string) XRAY>set echo ? end ECHO=TRUE {ON} XRAY>evaluate ($echo_old_sclib=$result) EVALUATE: symbol $ECHO_OLD_SCLIB set to TRUE (logical) XRAY>set echo=off message=off end Program version= 1.1 File version= 1.1 XRAY> XRAY> binresolution &low_res &high_res XRAY> mapresolution &high_res XRAY> XRAY> generate &low_res &high_res XGENER: generating reflections to produce a full set for the specified resolution range. XGENE2: 10271 new reflections have been generated. XRAY> XRAY> if ( &BLANK%reflection_infile_1 = false ) then NEXTCD: condition evaluated as true XRAY> reflection @@&reflection_infile_1 end ASSFIL: file 9ilb.hkl opened. REFLection> NREFlection= 9535 REFLection: data will be merged with existing data. REFLection> ANOMalous=FALSE REFLection> DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END XDECLARE: Object FOBS has been declared. REFLection> DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END XDECLARE: Object SIGMA has been declared. REFLection> DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END XDECLARE: Object TEST has been declared. REFLection> INDE 0 0 4 FOBS= 829.5 0.0 SIGMA= 9.05 TEST= 1 XSFAL: allocating space for complex reciprocal space object. XSFAL: allocating space for real reciprocal space object. XSFAL: allocating space for integer reciprocal space object. XRRR2: 591 new h,k,l indices have been added. XRAY> end if XRAY> if ( &BLANK%reflection_infile_2 = false ) then NEXTCD: condition evaluated as false XRAY> reflection @@&reflection_infile_2 end XRAY> end if XRAY> if ( &BLANK%reflection_infile_3 = false ) then NEXTCD: condition evaluated as false XRAY> reflection @@&reflection_infile_3 end XRAY> end if XRAY> XRAY> end CNSsolve> CNSsolve> if ( &BLANK%anom_library = false ) then NEXTCD: condition evaluated as false CNSsolve> @@&anom_library CNSsolve> else CNSsolve> set echo=off end ANOMalous=FALSe {OFF} NEXTCD: condition evaluated as false CNSsolve> end if CNSsolve> CNSsolve> set echo=off end NEXTCD: condition evaluated as false CNSsolve> CNSsolve> {- copy define parameters of optional arrays into symbols so CNSsolve> we can redefine them -} CNSsolve> CNSsolve> evaluate ($obs_i=&obs_i) EVALUATE: symbol $OBS_I set to "" (string) CNSsolve> evaluate ($obs_sigi=&obs_sigi) EVALUATE: symbol $OBS_SIGI set to "" (string) CNSsolve> evaluate ($obs_w=&obs_w) EVALUATE: symbol $OBS_W set to "" (string) CNSsolve> xray XRAY> @@CNS_XTALMODULE:checkrefinput ( ASSFIL: file /sw/share/xtal/cns_solve_1.1/modules/xtal/checkrefinput opened. XRAY>! Module file: checkrefinput XRAY>! XRAY>! CNS module XRAY>! ********** XRAY>! XRAY>! Authors: Axel Brunger and Paul Adams XRAY>! XRAY>! copyright Yale University XRAY>! XRAY>! Function: XRAY>! Checks the required input reciprocal space arrays XRAY>! XRAY>! Requirements: XRAY>! Needs to be called within xray XRAY> XRAY>module {checkrefinput} MODULE-DECLARATION> MODULE-DECLARATION>( MODULE-DECLARATION> &reftarget="residual"; {string} MODULE-DECLARATION> &obs_f; {reciprocal space array} MODULE-DECLARATION> &obs_sigf; {reciprocal space array} MODULE-DECLARATION> &test_set; {reciprocal space array} MODULE-DECLARATION> &obs_pa; {reciprocal space array} MODULE-DECLARATION> &obs_pb; {reciprocal space array} MODULE-DECLARATION> &obs_pc; {reciprocal space array} MODULE-DECLARATION> &obs_pd; {reciprocal space array} MODULE-DECLARATION> &obs_phase; {reciprocal space array} MODULE-DECLARATION> &obs_fom; {reciprocal space array} MODULE-DECLARATION> &obs_w; {reciprocal space array} MODULE-DECLARATION> &obs_i; {reciprocal space array} MODULE-DECLARATION> &obs_sigi; {reciprocal space array} MODULE-DECLARATION>) MODULE-INVOCATION> reftarget=&reftarget; &_2_REFTARGET set to &_1_REFTARGET MODULE-INVOCATION> obs_f=&obs_f; &_2_OBS_F set to &_1_OBS_F MODULE-INVOCATION> obs_sigf=&obs_sigf; &_2_OBS_SIGF set to &_1_OBS_SIGF MODULE-INVOCATION> test_set=&test_set; &_2_TEST_SET set to &_1_TEST_SET MODULE-INVOCATION> obs_pa=&obs_pa; &_2_OBS_PA set to &_1_OBS_PA MODULE-INVOCATION> obs_pb=&obs_pb; &_2_OBS_PB set to &_1_OBS_PB MODULE-INVOCATION> obs_pc=&obs_pc; &_2_OBS_PC set to &_1_OBS_PC MODULE-INVOCATION> obs_pd=&obs_pd; &_2_OBS_PD set to &_1_OBS_PD MODULE-INVOCATION> obs_phase=&obs_phase; &_2_OBS_PHASE set to &_1_OBS_PHASE MODULE-INVOCATION> obs_fom=&obs_fom; &_2_OBS_FOM set to &_1_OBS_FOM MODULE-INVOCATION> obs_w=$obs_w; &_2_OBS_W set to $_1_OBS_W MODULE-INVOCATION> obs_i=$obs_i; &_2_OBS_I set to $_1_OBS_I MODULE-INVOCATION> obs_sigi=$obs_sigi; &_2_OBS_SIGI set to $_1_OBS_SIGI MODULE-INVOCATION> ) XRAY> XRAY>set message ? end MESSage=NORM XRAY>evaluate ($message_old_cri=$result) EVALUATE: symbol $MESSAGE_OLD_CRI set to "NORM" (string) XRAY>set echo ? end ECHO=TRUE {ON} XRAY>evaluate ($echo_old_cri=$result) EVALUATE: symbol $ECHO_OLD_CRI set to TRUE (logical) XRAY>if ( $log_level = verbose ) then NEXTCD: condition evaluated as false XRAY> set echo=on message=normal end XRAY>else XRAY> set echo=off message=off end Program version= 1.1 File version= 1.1 XRAY> XRAY> query name=fcalc domain=reciprocal end Reciprocal space object FCALC does not exist. XRAY> if ( $object_exist = false ) then NEXTCD: condition evaluated as true XRAY> declare name=fcalc domain=reciprocal type=complex end XDECLARE: Object FCALC has been declared. XRAY> end if XRAY> declare name=fbulk domain=reciprocal type=complex end XDECLARE: Object FBULK has been declared. XRAY> XRAY> do (fbulk=0) ( all ) XREDUC: some reflection(s) converted to CNS standard asymm. unit. XREDU2: multiple instances found for some reflections. XREDU2: deleting redundant reflections. XREDU2: 591 reflections have been deleted. XREDU2: sorting all reflections. XSFAL: allocating space for complex reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> XRAY> query name=&STRIP%obs_f domain=reciprocal end Reciprocal space object FOBS exists, is used, and has type COMPLEX Object does not belong to any group. XRAY> declare name=fobs_orig domain=reciprocal type=$object_type end XDECLARE: Object FOBS_ORIG has been declared. XRAY> declare name=sigma_orig domain=reciprocal type=real end XDECLARE: Object SIGMA_ORIG has been declared. XRAY> XRAY> do (fobs_orig=&STRIP%obs_f) (all) XSFAL: allocating space for complex reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> do (sigma_orig=&STRIP%obs_sigf) (all) XSFAL: allocating space for real reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> XRAY> if ( &BLANK%obs_i = false ) then NEXTCD: condition evaluated as false XRAY> query name=&STRIP%obs_i domain=reciprocal end XRAY> declare name=iobs_orig domain=reciprocal type=$object_type end XRAY> declare name=sigi_orig domain=reciprocal type=real end XRAY> do (iobs_orig=&STRIP%obs_i) (all) XRAY> do (sigi_orig=&STRIP%obs_sigi) (all) XRAY> end if XRAY> XRAY> if ( &obs_type = "intensity" ) then NEXTCD: condition evaluated as false XRAY> if ( &BLANK%obs_i = true ) then XRAY> display Error: observed intensity array is undefined XRAY> display aborting script XRAY> abort XRAY> end if XRAY> evaluate ($reject_obs=&obs_i) XRAY> evaluate ($reject_sig=&obs_sigi) XRAY> show min (amplitude(&STRIP%obs_i)) (all) XRAY> evaluate ($obs_lower_limit=$result-0.1) XRAY> else XRAY> evaluate ($reject_obs=&obs_f) EVALUATE: symbol $REJECT_OBS set to "fobs" (string) XRAY> evaluate ($reject_sig=&obs_sigf) EVALUATE: symbol $REJECT_SIG set to "sigma" (string) XRAY> evaluate ($obs_lower_limit=0) EVALUATE: symbol $OBS_LOWER_LIMIT set to 0.00000 (real) XRAY> end if XRAY> XRAY> declare name=all_active domain=reciprocal type=integer end XDECLARE: Object ALL_ACTIVE has been declared. XRAY> declare name=ref_active domain=reciprocal type=integer end XDECLARE: Object REF_ACTIVE has been declared. XRAY> declare name=map_active domain=reciprocal type=integer end XDECLARE: Object MAP_ACTIVE has been declared. XRAY> declare name=tst_active domain=reciprocal type=integer end XDECLARE: Object TST_ACTIVE has been declared. XRAY> XRAY> do (all_active=0) ( all ) XSFAL: allocating space for integer reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> do (all_active=1) ( &low_res >= d >= &high_res ) Total of 10271 structure factor elements were selected. XRAY> XRAY> do (ref_active=0) ( all ) XSFAL: allocating space for integer reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> do (ref_active=1) ( ( amplitude($STRIP%reject_obs) > $obs_lower_limit ) and DO> ( &refine_low_res >= d >= &high_res ) ) Total of 9535 structure factor elements were selected. XRAY> XRAY> do (map_active=0) ( all ) XSFAL: allocating space for integer reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> do (map_active=1) ( ( amplitude($STRIP%reject_obs) > $obs_lower_limit ) and DO> ( &low_res >= d >= &high_res ) ) Total of 9535 structure factor elements were selected. XRAY> XRAY> statistics overall STATistics> completeness STATistics> selection=( map_active=1 ) Total of 9535 structure factor elements were selected. STATistics> end #bin | resolution range | #refl | 1 2.30 500.01 9535 0.9283 XRAY> evaluate ($total_compl=$expression1) EVALUATE: symbol $TOTAL_COMPL set to 0.928342 (real) XRAY> XRAY> show sum (1) ( map_active=1 ) Sum of 9535 elements = 9535.0000 XRAY> evaluate ($total_read=$select) EVALUATE: symbol $TOTAL_READ set to 9535.00 (real) XRAY> evaluate ($total_theor=int(1./$total_compl * $total_read)) EVALUATE: symbol $TOTAL_THEOR set to 10271.0 (real) XRAY> XRAY> show rms (amplitude($STRIP%reject_obs)) ( ref_active=1 ) Rms of 9535 elements = 112.4132 XRAY> evaluate ($obs_high=$result*&obs_rms) EVALUATE: symbol $OBS_HIGH set to 0.112413E+07 (real) XRAY> show min (amplitude($STRIP%reject_obs)) ( ref_active=1 ) Minimum of 9535 elements = 16.3000 XRAY> evaluate ($obs_low=$result) EVALUATE: symbol $OBS_LOW set to 16.3000 (real) XRAY> XRAY> do (ref_active=0) ( all ) Total of 10271 structure factor elements were selected. XRAY> do (ref_active=1) DO> ( ( amplitude($STRIP%reject_obs) >= &sigma_cut*$STRIP%reject_sig ) and DO> ( $STRIP%reject_sig # 0 ) and DO> ( $obs_low <= amplitude($STRIP%reject_obs) <= $obs_high ) and DO> ( &refine_low_res >= d >= &high_res ) ) Total of 9535 structure factor elements were selected. XRAY> XRAY> do (tst_active=0) (all) XSFAL: allocating space for integer reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> if ( &BLANK%test_set = false ) then NEXTCD: condition evaluated as true XRAY> do (tst_active=1) (map_active=1 and &STRIP%test_set=&test_flag) Total of 959 structure factor elements were selected. XRAY> end if XRAY> XRAY> show rms (amplitude($STRIP%reject_obs)) ( map_active=1 ) Rms of 9535 elements = 112.4132 XRAY> evaluate ($obs_high=$result*&obs_rms) EVALUATE: symbol $OBS_HIGH set to 0.112413E+07 (real) XRAY> show min (amplitude($STRIP%reject_obs)) ( map_active=1 ) Minimum of 9535 elements = 16.3000 XRAY> evaluate ($obs_low=$result) EVALUATE: symbol $OBS_LOW set to 16.3000 (real) XRAY> XRAY> do (map_active=0) ( all ) Total of 10271 structure factor elements were selected. XRAY> do (map_active=1) DO> ( ( amplitude($STRIP%reject_obs) >= &sigma_cut*$STRIP%reject_sig ) and DO> ( $STRIP%reject_sig # 0 ) and DO> ( $obs_low <= amplitude($STRIP%reject_obs) <= $obs_high ) and DO> ( &low_res >= d >= &high_res ) ) Total of 9535 structure factor elements were selected. XRAY> XRAY> show sum (1) ( map_active=1 and tst_active=0 ) Sum of 8576 elements = 8576.0000 XRAY> evaluate ($total_work=$select) EVALUATE: symbol $TOTAL_WORK set to 8576.00 (real) XRAY> show sum (1) ( map_active=1 and tst_active=1 ) Sum of 959 elements = 959.0000 XRAY> evaluate ($total_test=$select) EVALUATE: symbol $TOTAL_TEST set to 959.000 (real) XRAY> evaluate ($total_used=$total_work+$total_test) EVALUATE: symbol $TOTAL_USED set to 9535.00 (real) XRAY> XRAY> evaluate ($unobserved=$total_theor-$total_read) EVALUATE: symbol $UNOBSERVED set to 736.000 (real) XRAY> evaluate ($rejected=$total_read-$total_used) EVALUATE: symbol $REJECTED set to 0.00000 (real) XRAY> evaluate ($per_unobs=100*($unobserved/$total_theor)) EVALUATE: symbol $PER_UNOBS set to 7.16581 (real) XRAY> evaluate ($per_reject=100*($rejected/$total_theor)) EVALUATE: symbol $PER_REJECT set to 0.00000 (real) XRAY> evaluate ($per_used=100*($total_used/$total_theor)) EVALUATE: symbol $PER_USED set to 92.8342 (real) XRAY> evaluate ($per_work=100*($total_work/$total_theor)) EVALUATE: symbol $PER_WORK set to 83.4972 (real) XRAY> evaluate ($per_test=100*($total_test/$total_theor)) EVALUATE: symbol $PER_TEST set to 9.33697 (real) XRAY> XRAY> associate fcalc ( &atom_select ) SELRPN: 1275 atoms have been selected out of 1275 XRAY> XRAY> tselection=( map_active=1 ) XRAY> XRAY> cvselection=( tst_active=1 ) XRAY> XRAY> method=FFT XRAY> XRAY> fft XFFT> grid=&grid XFFT> if ( &fft_memory < 0 ) then NEXTCD: condition evaluated as true XFFT> automemory=true XFFT> else XFFT> memory=&fft_memory XFFT> end if XFFT> end XRAY> XRAY> if ( &wa >= 0 ) then NEXTCD: condition evaluated as false XRAY> wa=&wa XRAY> end if XRAY> XRAY> end CNSsolve> CNSsolve> if ( &map_type = "observed" ) then NEXTCD: condition evaluated as false CNSsolve> evalaute ($test_hl=true) CNSsolve> elseif ( &map_type = "combined" ) then NEXTCD: condition evaluated as false CNSsolve> evalaute ($test_hl=true) CNSsolve> else CNSsolve> evalaute ($test_hl=false) EVALUATE: symbol $TEST_HL set to FALSE (logical) CNSsolve> end if CNSsolve> CNSsolve> if ( $test_hl = true ) then NEXTCD: condition evaluated as false CNSsolve> xray CNSsolve> @@CNS_XTALMODULE:check_abcd (pa=&obs_pa; CNSsolve> pb=&obs_pb; CNSsolve> pc=&obs_pc; CNSsolve> pd=&obs_pd;) CNSsolve> end CNSsolve> end if CNSsolve> CNSsolve> if ( &BLANK%ncs_infile = false ) then NEXTCD: condition evaluated as false CNSsolve> inline @&ncs_infile CNSsolve> end if CNSsolve> CNSsolve> if ( &BLANK%restraints_infile = false ) then NEXTCD: condition evaluated as false CNSsolve> @&restraints_infile CNSsolve> end if CNSsolve> CNSsolve> do (store7=0) (all) SELRPN: 1275 atoms have been selected out of 1275 CNSsolve> CNSsolve> evaluate ($nalt=1) EVALUATE: symbol $NALT set to 1.00000 (real) CNSsolve> evaluate ($alt=1) EVALUATE: symbol $ALT set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop nalt NEXTCD: condition evaluated as true CNSsolve> if ( &exist_conf_$alt = true ) then NEXTCD: condition evaluated as true CNSsolve> show sum(1) ( &conf_$alt ) SELRPN: 0 atoms have been selected out of 1275 SHOW: zero atoms selected CNSsolve> if ( $result > 0 ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($nalt=$nalt+1) CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> evaluate ($nalt=$nalt-1) CNSsolve> end if CNSsolve> evaluate ($alt=$alt+1) EVALUATE: symbol $ALT set to 2.00000 (real) CNSsolve> end loop nalt CNSsolve> while ( $done = false ) loop nalt NEXTCD: condition evaluated as true CNSsolve> if ( &exist_conf_$alt = true ) then NEXTCD: condition evaluated as true CNSsolve> show sum(1) ( &conf_$alt ) SELRPN: 0 atoms have been selected out of 1275 SHOW: zero atoms selected CNSsolve> if ( $result > 0 ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($nalt=$nalt+1) CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> evaluate ($nalt=$nalt-1) CNSsolve> end if CNSsolve> evaluate ($alt=$alt+1) EVALUATE: symbol $ALT set to 3.00000 (real) CNSsolve> end loop nalt CNSsolve> while ( $done = false ) loop nalt NEXTCD: condition evaluated as true CNSsolve> if ( &exist_conf_$alt = true ) then NEXTCD: condition evaluated as true CNSsolve> show sum(1) ( &conf_$alt ) SELRPN: 0 atoms have been selected out of 1275 SHOW: zero atoms selected CNSsolve> if ( $result > 0 ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($nalt=$nalt+1) CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> evaluate ($nalt=$nalt-1) CNSsolve> end if CNSsolve> evaluate ($alt=$alt+1) EVALUATE: symbol $ALT set to 4.00000 (real) CNSsolve> end loop nalt CNSsolve> while ( $done = false ) loop nalt NEXTCD: condition evaluated as true CNSsolve> if ( &exist_conf_$alt = true ) then NEXTCD: condition evaluated as true CNSsolve> show sum(1) ( &conf_$alt ) SELRPN: 0 atoms have been selected out of 1275 SHOW: zero atoms selected CNSsolve> if ( $result > 0 ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($nalt=$nalt+1) CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> evaluate ($nalt=$nalt-1) CNSsolve> end if CNSsolve> evaluate ($alt=$alt+1) EVALUATE: symbol $ALT set to 5.00000 (real) CNSsolve> end loop nalt CNSsolve> while ( $done = false ) loop nalt NEXTCD: condition evaluated as true CNSsolve> if ( &exist_conf_$alt = true ) then NEXTCD: condition evaluated as false CNSsolve> show sum(1) ( &conf_$alt ) CNSsolve> if ( $result > 0 ) then CNSsolve> evaluate ($nalt=$nalt+1) CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> evaluate ($nalt=$nalt-1) EVALUATE: symbol $NALT set to 0.00000 (real) CNSsolve> end if CNSsolve> evaluate ($alt=$alt+1) EVALUATE: symbol $ALT set to 6.00000 (real) CNSsolve> end loop nalt CNSsolve> while ( $done = false ) loop nalt NEXTCD: condition evaluated as false CNSsolve> if ( &exist_conf_$alt = true ) then CNSsolve> show sum(1) ( &conf_$alt ) CNSsolve> if ( $result > 0 ) then CNSsolve> evaluate ($nalt=$nalt+1) CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> evaluate ($nalt=$nalt-1) CNSsolve> end if CNSsolve> evaluate ($alt=$alt+1) CNSsolve> end loop nalt CNSsolve> CNSsolve> evaluate ($alt=1) EVALUATE: symbol $ALT set to 1.00000 (real) CNSsolve> while ( $alt <= $nalt ) loop alt NEXTCD: condition evaluated as false CNSsolve> do (store7=$alt) ( &conf_$alt ) CNSsolve> evaluate ($alt=$alt+1) CNSsolve> end loop alt CNSsolve> CNSsolve> ident ( store8 ) ( byresidue ( &atom_omit saround &sphere ) ) SELRPN: 0 atoms have been selected out of 1275 CNSsolve> CNSsolve> ident ( store9 ) ( byresidue ( ( store8 ) saround &cushion and SELRPN> not store8 ) ) SELRPN: 0 atoms have been selected out of 1275 CNSsolve> CNSsolve> igroup IGROup> interaction ( &atom_select and not(attr store7 > 0)) SELRPN: 1275 atoms have been selected out of 1275 SELRPN> ( &atom_select and not(attr store7 > 0)) SELRPN: 1275 atoms have been selected out of 1275 IGROup> evaluate ($alt=1) EVALUATE: symbol $ALT set to 1.00000 (real) IGROup> while ( $alt <= $nalt ) loop alcs NEXTCD: condition evaluated as false IGROup> interaction ( &atom_select and IGROup> ( attr store7 = $alt or attr store7 = 0 )) IGROup> ( &atom_select and ( attr store7 = $alt )) IGROup> evaluate ($alt=$alt+1) IGROup> end loop alcs IGROup> end CNSsolve> CNSsolve> {- check isolated atoms and atoms at special positions and add to CNSsolve> list of fixed atoms if needed - store7 will be used -} CNSsolve> CNSsolve> if (&anneal=true) then NEXTCD: condition evaluated as true CNSsolve> evaluate ($mode=&md_type) EVALUATE: symbol $MODE set to "torsion" (string) CNSsolve> else CNSsolve> evaluate ($mode="minimization") CNSsolve> end if CNSsolve> CNSsolve> @CNS_XTALMODULE:setupfixed ( ASSFIL: file /sw/share/xtal/cns_solve_1.1/modules/xtal/setupfixed opened. CNSsolve>! Module file: setupfixed CNSsolve>! CNSsolve>! CNS module CNSsolve>! ********** CNSsolve>! CNSsolve>! Authors: Axel Brunger CNSsolve>! CNSsolve>! copyright Yale University CNSsolve>! CNSsolve>! Function: CNSsolve>! CNSsolve>! Sets up fixed atom selection and CNSsolve>! performs various checks for CNSsolve>! 1. isolated atoms CNSsolve>! 2. isolated di-atomic molecules CNSsolve>! 3. atoms at special positions CNSsolve>! CNSsolve>! Adds isolated atoms, diatomic molecules, and/or special-position atoms to the CNSsolve>! fixed atom selection. CNSsolve>! CNSsolve>! Requirements: CNSsolve>! Needs to be called from cns main level CNSsolve> CNSsolve>module {setupfixed} MODULE-DECLARATION> MODULE-DECLARATION>( MODULE-DECLARATION> &mode; {string} {"minimization", "cartesian", "torsion"} MODULE-DECLARATION> &atom_select; {selection } {input: all selected atoms for refinement} MODULE-DECLARATION> &atom_fixed; {selection } {input: explicitly fixed atoms} MODULE-DECLARATION> &atom_total_fixed; {atomic property array } {output: all fixed atoms} MODULE-DECLARATION> &atom_multiplicity; {atomic property array } {output: multiplicity of atoms} MODULE-DECLARATION> &mset=$mset; {symbol} {output: number of disconnected sets} MODULE-DECLARATION> MODULE-DECLARATION>) MODULE-INVOCATION> mode=$mode; &_2_MODE set to $_1_MODE MODULE-INVOCATION> atom_select=&atom_select; &_2_ATOM_SELECT set to &_1_ATOM_SELECT MODULE-INVOCATION> atom_fixed=&atom_fixed; &_2_ATOM_FIXED set to &_1_ATOM_FIXED MODULE-INVOCATION> atom_total_fixed=store7; &_2_ATOM_TOTAL_FIXED set to store7 MODULE-INVOCATION> atom_multiplicity=rmsd; &_2_ATOM_MULTIPLICITY set to rmsd MODULE-INVOCATION> mset=$mset; &_2_MSET set to $_1_MSET MODULE-INVOCATION> ) CNSsolve> CNSsolve> set message ? end MESSage=NORM CNSsolve> evaluate ($message_old_fix=$result) EVALUATE: symbol $MESSAGE_OLD_FIX set to "NORM" (string) CNSsolve> set echo ? end ECHO=TRUE {ON} CNSsolve> evaluate ($echo_old_fix=$result) EVALUATE: symbol $ECHO_OLD_FIX set to TRUE (logical) CNSsolve> if ( $log_level = verbose ) then NEXTCD: condition evaluated as false CNSsolve> set echo=on message=normal end CNSsolve> else CNSsolve> set echo=off message=off end Program version= 1.1 File version= 1.1 CONNECt: selected atoms form 57 covalently disconnected set(s) list of isolated (non-covalently bonded) atoms: ( HOH 201 O ) O ( HOH 202 O ) O ( HOH 203 O ) O ( HOH 204 O ) O ( HOH 205 O ) O ( HOH 206 O ) O ( HOH 207 O ) O ( HOH 208 O ) O ( HOH 209 O ) O ( HOH 210 O ) O ( HOH 211 O ) O ( HOH 212 O ) O ( HOH 213 O ) O ( HOH 214 O ) O ( HOH 215 O ) O ( HOH 216 O ) O ( HOH 217 O ) O ( HOH 218 O ) O ( HOH 219 O ) O ( HOH 220 O ) O ( HOH 221 O ) O ( HOH 222 O ) O ( HOH 223 O ) O ( HOH 224 O ) O ( HOH 225 O ) O ( HOH 226 O ) O ( HOH 227 O ) O ( HOH 228 O ) O ( HOH 229 O ) O ( HOH 230 O ) O ( HOH 231 O ) O ( HOH 232 O ) O ( HOH 233 O ) O ( HOH 234 O ) O ( HOH 235 O ) O ( HOH 236 O ) O ( HOH 237 O ) O ( HOH 238 O ) O ( HOH 239 O ) O ( HOH 240 O ) O ( HOH 241 O ) O ( HOH 242 O ) O ( HOH 243 O ) O ( HOH 244 O ) O ( HOH 245 O ) O ( HOH 246 O ) O ( HOH 247 O ) O ( HOH 248 O ) O ( HOH 249 O ) O ( HOH 250 O ) O ( HOH 251 O ) O ( HOH 252 O ) O ( HOH 253 O ) O ( HOH 254 O ) O ( HOH 255 O ) O ( HOH 256 O ) O list of isolated (non-covalently bonded) di-atomic molecules: --none-- list of atoms at special positions: --none-- 56 isolated atoms, atoms in di-atomic molecules, atoms at special positions, explicitly fixed atoms, and atoms not selected for refinement will be fixed. CNSsolve> CNSsolve> fix selection=( store7 ) end SELRPN: 56 atoms have been selected out of 1275 CNSsolve> CNSsolve> xray XRAY> associate fcalc ( &atom_select and not store8 ) SELRPN: 1275 atoms have been selected out of 1275 XRAY> end CNSsolve> CNSsolve> fastnb grid end CNSsolve> CNSsolve> flags FLAGS> exclude elec include pvdw xref FLAGS> ? EFLAGS: the following energy flags are set EFLAGS: BOND ANGL DIHE IMPR VDW PVDW XREF FLAGS> end CNSsolve> CNSsolve> set seed=&seed end CNSsolve> CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> evaluate ($start_temp=&temperature) EVALUATE: symbol $START_TEMP set to 1000.00 (real) CNSsolve> evaluate ($time_step=0.004) EVALUATE: symbol $TIME_STEP set to 0.400000E-02 (real) CNSsolve> evaluate ($md_steps=6) EVALUATE: symbol $MD_STEPS set to 6.00000 (real) CNSsolve> evaluate ($fbeta=200) EVALUATE: symbol $FBETA set to 200.000 (real) CNSsolve> end if CNSsolve> CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($start_temp=&temperature) CNSsolve> evaluate ($time_step=0.0005) CNSsolve> evaluate ($md_steps=50) CNSsolve> evaluate ($fbeta=100) CNSsolve> end if CNSsolve> CNSsolve> evaluate ($struct=1) EVALUATE: symbol $STRUCT set to 1.00000 (real) CNSsolve> evaluate ($done=false) EVALUATE: symbol $DONE set to FALSE (logical) CNSsolve> while ( $done = false ) loop struct NEXTCD: condition evaluated as true CNSsolve> if ( &exist_coordinate_infile_$struct = true ) then NEXTCD: condition evaluated as true CNSsolve> if ( &BLANK%coordinate_infile_$struct = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($done=true) CNSsolve> evaluate ($struct=$struct-1) CNSsolve> else CNSsolve> evaluate ($struct=$struct+1) EVALUATE: symbol $STRUCT set to 2.00000 (real) CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> evaluate ($struct=$struct-1) CNSsolve> end if CNSsolve> end loop struct CNSsolve> while ( $done = false ) loop struct NEXTCD: condition evaluated as true CNSsolve> if ( &exist_coordinate_infile_$struct = true ) then NEXTCD: condition evaluated as false CNSsolve> if ( &BLANK%coordinate_infile_$struct = true ) then CNSsolve> evaluate ($done=true) CNSsolve> evaluate ($struct=$struct-1) CNSsolve> else CNSsolve> evaluate ($struct=$struct+1) CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) EVALUATE: symbol $DONE set to TRUE (logical) CNSsolve> evaluate ($struct=$struct-1) EVALUATE: symbol $STRUCT set to 1.00000 (real) CNSsolve> end if CNSsolve> end loop struct CNSsolve> while ( $done = false ) loop struct NEXTCD: condition evaluated as false CNSsolve> if ( &exist_coordinate_infile_$struct = true ) then CNSsolve> if ( &BLANK%coordinate_infile_$struct = true ) then CNSsolve> evaluate ($done=true) CNSsolve> evaluate ($struct=$struct-1) CNSsolve> else CNSsolve> evaluate ($struct=$struct+1) CNSsolve> end if CNSsolve> else CNSsolve> evaluate ($done=true) CNSsolve> evaluate ($struct=$struct-1) CNSsolve> end if CNSsolve> end loop struct CNSsolve> CNSsolve> evaluate ($ave_cycle=$struct) EVALUATE: symbol $AVE_CYCLE set to 1.00000 (real) CNSsolve> CNSsolve> evaluate ($cycle=1) EVALUATE: symbol $CYCLE set to 1.00000 (real) CNSsolve> CNSsolve> xray XRAY> declare name=dtarg domain=reciprocal type=complex end XDECLARE: Object DTARG has been declared. XRAY> declare name=fcave domain=reciprocal type=complex end XDECLARE: Object FCAVE has been declared. XRAY> declare name=fpave domain=reciprocal type=complex end XDECLARE: Object FPAVE has been declared. XRAY> query name=&STRIP%obs_f domain=reciprocal end Reciprocal space object FOBS exists, is used, and has type COMPLEX Object does not belong to any group. XRAY> declare name=foave domain=reciprocal type=$object_type end XDECLARE: Object FOAVE has been declared. XRAY> declare name=dave domain=reciprocal type=complex end XDECLARE: Object DAVE has been declared. XRAY> declare name=total domain=reciprocal type=complex end XDECLARE: Object TOTAL has been declared. XRAY> declare name=fmap domain=reciprocal type=complex end XDECLARE: Object FMAP has been declared. XRAY> do (fcave=0) (all) XSFAL: allocating space for complex reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> do (fpave=0) (all) XSFAL: allocating space for complex reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> do (foave=0) (all) XSFAL: allocating space for complex reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> do (dave=0) (all) XSFAL: allocating space for complex reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> end CNSsolve> CNSsolve> while ( $cycle <= $ave_cycle ) loop main NEXTCD: condition evaluated as true CNSsolve> CNSsolve> coord init end COOR: selected main coordinates initialized CNSsolve> coord @@&coordinate_infile_$cycle ASSFIL: file refine-0-2_mtf.pdb opened. COOR>REMARK FILENAME="refine-0-2_mtf.pdb" COOR>REMARK DATE:15-Sep-2005 09:31:20 created by user: mdepristo COOR>REMARK VERSION:1.1 COOR>ATOM 1 CB ALA A 1 -17.953 16.662 -22.034 1.00 58.44 A COOR>ATOM 2 C ALA A 1 -20.198 17.727 -22.156 1.00 56.81 A CNSsolve> CNSsolve> xray XRAY> do (&STRIP%obs_f=fobs_orig) (all) Total of 10271 structure factor elements were selected. XRAY> do (&STRIP%obs_sigf=sigma_orig) (all) Total of 10271 structure factor elements were selected. XRAY> if ( &BLANK%obs_i = false ) then NEXTCD: condition evaluated as false XRAY> do (&STRIP%obs_i=iobs_orig) (all) XRAY> do (&STRIP%obs_sigi=sigi_orig) (all) XRAY> end if XRAY> end CNSsolve> CNSsolve> xray XRAY> predict PREDict> mode=reciprocal PREDict> to=fcalc PREDict> selection=( all_active=1 ) Total of 10271 structure factor elements were selected. PREDict> atomselection=( &atom_select and not store8 ) SELRPN: 1275 atoms have been selected out of 1275 PREDict> end FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XSFAL: allocating space for complex reciprocal space object. %XFFT-AUTOmem: increasing memory allocation to 2000000 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XRAY> end CNSsolve> CNSsolve> @@CNS_XTALMODULE:scalenbulk (bscale=&bscale; ASSFIL: file /sw/share/xtal/cns_solve_1.1/modules/xtal/scalenbulk opened. CNSsolve>! Module file: scalenbulk CNSsolve>! CNSsolve>! Function: applies wilson-type scaling between Fobs and Fcalc CNSsolve>! and also applies bulk-solvent correction if requested. CNSsolve>! Anisotropic scaling possible. CNSsolve>! CNSsolve>! CNSsolve>! CNS module CNSsolve>! ********** CNSsolve>! CNSsolve>! Authors: Axel T. Brunger and Paul D. Adams CNSsolve>! CNSsolve>! copyright Yale University CNSsolve>! CNSsolve>! Requirements: CNSsolve>! This module can only be used from the main level of CNS. CNSsolve>! CNSsolve> CNSsolve>module {scalenbulk} MODULE-DECLARATION>( MODULE-DECLARATION> MODULE-DECLARATION> !input: MODULE-DECLARATION> MODULE-DECLARATION> &bscale="no"; {"no" | "isotropic" | "anisotropic" | MODULE-DECLARATION> "anisotropic_fixed_isotropic"} MODULE-DECLARATION> &sel=all; {all active structure factors} MODULE-DECLARATION> &sel_test=none; {test set reflections} MODULE-DECLARATION> &res_bscale=6.0; {lower resolution limit for calculation of MODULE-DECLARATION> B-factor correction} MODULE-DECLARATION> &atom_select=( all ); {atom selection} MODULE-DECLARATION> &bulk_sol=false; {true or false (type logical) bulk solvent correction} MODULE-DECLARATION> &bulk_mask=""; {mask for bulk solvent - from file if name given, MODULE-DECLARATION> otherwise from coords of atoms selected (type: string)} MODULE-DECLARATION> &bulk_atoms=( all ); {atoms used to create solvent mask} MODULE-DECLARATION> &sol_k=-1; {optional: fix solvent density level by setting this MODULE-DECLARATION> parameter to a positive value} MODULE-DECLARATION> &sol_b=-1; {optional: fix solvent B factor by setting this MODULE-DECLARATION> parameter to a positive value} MODULE-DECLARATION> &fcalc=fcalc; {name of structure factor array - scaling will be MODULE-DECLARATION> applied} MODULE-DECLARATION> &fobs=fobs; {observed amplitude data - only anisotropic part will MODULE-DECLARATION> be applied} MODULE-DECLARATION> &sigma=sigma; {name of corresponding sigma array} MODULE-DECLARATION> &iobs=iobs; {observed intensity data - only anisotropic part will MODULE-DECLARATION> be applied} MODULE-DECLARATION> &sigi=sigi; {name of corresponding sigma array} MODULE-DECLARATION> &fpart=fpart; {bulk solvent structure factors} MODULE-DECLARATION> MODULE-DECLARATION> ! output: MODULE-DECLARATION> &B2_11=$B2_11; {output: overall anisotropic tensor} MODULE-DECLARATION> &B2_22=$B2_22; {note: trace will be zero (isotropic} MODULE-DECLARATION> &B2_33=$B2_33; { contribution is applied to the atomic B array} MODULE-DECLARATION> &B2_12=$B2_12; MODULE-DECLARATION> &B2_13=$B2_13; MODULE-DECLARATION> &B2_23=$B2_23; MODULE-DECLARATION> &sol_k_ref=$sol_k_ref; MODULE-DECLARATION> &sol_b_ref=$sol_b_ref; MODULE-DECLARATION> &trace=$trace; {the trace of the anisotropic correction tensor} MODULE-DECLARATION> MODULE-DECLARATION> ! The inverse of the tensor is applied to &fobs, &iobs, &sigma and &sigi MODULE-DECLARATION> MODULE-DECLARATION> ! The overall isotropic B contribution is applied to the atomic MODULE-DECLARATION> ! B array with "aniso" option, with "aniso-iso" option no isotropic MODULE-DECLARATION> ! correction is applied MODULE-DECLARATION> MODULE-DECLARATION> &b_too_low=false; {does the correction produce low atomic B-values?} MODULE-DECLARATION> {those B-values lower than 0 will be set to 0} MODULE-DECLARATION> ) &_2_BSCALE set to &_1_BSCALE MODULE-INVOCATION> sel=( ref_active=1 ); &_2_SEL set to ( ref_active = 1 ) MODULE-INVOCATION> sel_test=( tst_active=1 ); &_2_SEL_TEST set to ( tst_active = 1 ) MODULE-INVOCATION> res_bscale=&low_res_bscale; &_2_RES_BSCALE set to &_1_LOW_RES_BSCALE MODULE-INVOCATION> atom_select=( &atom_select ); &_2_ATOM_SELECT set to ( &_1_ATOM_SELECT ) MODULE-INVOCATION> bulk_sol=&bulk_sol; &_2_BULK_SOL set to &_1_BULK_SOL MODULE-INVOCATION> bulk_mask=&bulk_mask_infile; &_2_BULK_MASK set to &_1_BULK_MASK_INFILE MODULE-INVOCATION> bulk_atoms=( &atom_select ); &_2_BULK_ATOMS set to ( &_1_ATOM_SELECT ) MODULE-INVOCATION> sol_k=&sol_k; &_2_SOL_K set to &_1_SOL_K MODULE-INVOCATION> sol_b=&sol_b; &_2_SOL_B set to &_1_SOL_B MODULE-INVOCATION> fcalc=fcalc; &_2_FCALC set to fcalc MODULE-INVOCATION> fobs=&STRIP%obs_f; &_2_FOBS set to &STRIP%_1_OBS_F MODULE-INVOCATION> sigma=&STRIP%obs_sigf; &_2_SIGMA set to &STRIP%_1_OBS_SIGF MODULE-INVOCATION> iobs=$STRIP%obs_i; &_2_IOBS set to $STRIP%_1_OBS_I MODULE-INVOCATION> sigi=$STRIP%obs_sigi; &_2_SIGI set to $STRIP%_1_OBS_SIGI MODULE-INVOCATION> fpart=fbulk; &_2_FPART set to fbulk MODULE-INVOCATION> B2_11=$aniso_11; &_2_B2_11 set to $_1_ANISO_11 MODULE-INVOCATION> B2_22=$aniso_22; &_2_B2_22 set to $_1_ANISO_22 MODULE-INVOCATION> B2_33=$aniso_33; &_2_B2_33 set to $_1_ANISO_33 MODULE-INVOCATION> B2_12=$aniso_12; &_2_B2_12 set to $_1_ANISO_12 MODULE-INVOCATION> B2_13=$aniso_13; &_2_B2_13 set to $_1_ANISO_13 MODULE-INVOCATION> B2_23=$aniso_23; &_2_B2_23 set to $_1_ANISO_23 MODULE-INVOCATION> trace=$trace; &_2_TRACE set to $_1_TRACE MODULE-INVOCATION> sol_k_ref=$sol_k_ref; &_2_SOL_K_REF set to $_1_SOL_K_REF MODULE-INVOCATION> sol_b_ref=$sol_b_ref; &_2_SOL_B_REF set to $_1_SOL_B_REF MODULE-INVOCATION> b_too_low=$low_b_flag;) &_2_B_TOO_LOW set to $_1_LOW_B_FLAG CNSsolve> CNSsolve> set message ? end MESSage=NORM CNSsolve> evaluate ($message_old=$result) EVALUATE: symbol $MESSAGE_OLD set to "NORM" (string) CNSsolve> set echo ? end ECHO=TRUE {ON} CNSsolve> evaluate ($echo_old=$result) EVALUATE: symbol $ECHO_OLD set to TRUE (logical) CNSsolve> if ( $log_level = verbose ) then NEXTCD: condition evaluated as false CNSsolve> set echo=on message=normal end CNSsolve> else CNSsolve> set echo=off message=off end Program version= 1.1 File version= 1.1 XSCALE: total number of data sets were selected 2 XSCALE: set 1 FOBS is specified as the target data set XSCLSQ: ---------------------- Cycle 0 0.0100 ---------------------- XSCLSQ: Target= 0.1182 Scale= 0.928 R-factor= 0.3105 XSCLSQ: set 1 FOBS kscal= -1.000 bscal_tensor= XSCLSQ: B11= 0.00 B22= 0.00 B33= 0.00 B12= 0.00 B13= 0.00 B23= 0.00 XSCLSQ: set 2 FCALC kscal= 1.000 bscal_tensor= XSCLSQ: B11= 0.00 B22= 0.00 B33= 0.00 B12= 0.00 B13= 0.00 B23= 0.00 XSCLSQ: ---------------------- Cycle 1 0.0100 ---------------------- XSCLSQ: Target= 0.1170 Scale= 0.929 R-factor= 0.3098 XSCLSQ: set 1 FOBS kscal= -1.000 bscal_tensor= XSCLSQ: B11= 0.00 B22= 0.00 B33= 0.00 B12= 0.00 B13= 0.00 B23= 0.00 XSCLSQ: set 2 FCALC kscal= 0.934 bscal_tensor= XSCLSQ: B11= -4.51 B22= -4.51 B33= -2.40 B12= 0.00 B13= 0.00 B23= 0.00 XSCLSQ: ---------------------- Cycle 2 0.0010 ---------------------- XSCLSQ: Target= 0.1170 Scale= 0.929 R-factor= 0.3097 XSCLSQ: set 1 FOBS kscal= -1.000 bscal_tensor= XSCLSQ: B11= 0.00 B22= 0.00 B33= 0.00 B12= 0.00 B13= 0.00 B23= 0.00 XSCLSQ: set 2 FCALC kscal= 0.936 bscal_tensor= XSCLSQ: B11= -4.38 B22= -4.38 B33= -2.38 B12= 0.00 B13= 0.00 B23= 0.00 XSCALE: ---------------------- Final ------------------------------------ XSCALE: Target= 0.1170 Scale= 0.929 R-factor= 0.3097 XSCALE: normal termination - convergence. XSCALE: K has been multiplied by the overall scale ($XSCFFK) 0.929 MULTiscale: SET K B_tensor 1 FOBS -1.0000 B11= 0.000 B22= 0.000 B33= 0.000 B12= 0.000 B13= 0.000 B23= 0.000 2 FCALC 0.8695 B11= -4.385 B22= -4.385 B33= -2.377 B12= 0.000 B13= 0.000 B23= 0.000 MULTiscale: K is stored in symbols $K, and B_tensor MULTiscale: are stored in $B_11, $B_22, $B_33, etc. MULTiscale: the overall scale is stored in symbol $XSCFFK Trace/3 of the B-factor tensor has been subtraced from the B-factor atomic property array. The B-factor tensor has been modified to make the trace zero. modified tensor: B11= 0.669 B22= 0.669 B33= -1.338 B12= 0.000 B13= 0.000 B23= 0.000 XMASK: 1275 atoms have been selected for mask calculation. Minimum brick that covers asymmetric unit: A= 0,..., 48 B= 0,..., 48 C= 0,..., 144 XMASK: average mask radius around selected atoms 1.6795 A XMASK: probe radius= 1.0000 shrink radius= 1.0000 XMASK: volume inside mask= 36.3170% (MASK<=0) XMASK: volume outside mask= 63.6830% (MASK=1) |--------------------------- MULTiscale parameters --------------------------- | least-squares: NCYC= 30 DIAG= 0 EPS= 0.0010 | initials: KINI= 1.000 BINI= 0.000 | restraints: KSMIn= 0.000 BMIN= 10.000 BMAX= 300.000 | two resolution-dependent scales are applied. RESK= 5.000 | MULTiscale: SET K B | 1 FOBS -1.0000 0.0000 | 2 FCALC 1.0000 0.0000 | 3 FBULK -9999.0000 -9999.0000 |------------------------------------------------------------------------------ XSCALE: total number of data sets were selected 3 XSCALE: set 1 FOBS is specified as the target data set XSCLSQ: ---------------------- Cycle 0 0.0100 ---------------------- XSCLSQ: Target= 0.5467 Scale= 0.397 R-factor= 0.5585 XSCLSQ: T-low = 0.1899 Scale= 0.210 R-factor= 0.7386 XSCLSQ: T-high= 0.1758 Scale= 0.734 R-factor= 0.4418 XSCLSQ: set 1 FOBS kscal= -1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 2 FCALC kscal= 1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 3 FBULK kscal= 1.000 bscal= 0.00 0.000 0.00 XSCLSQ: ---------------------- Cycle 1 0.0100 ---------------------- XSCLSQ: Target= 0.4717 Scale= 0.513 R-factor= 0.4989 XSCLSQ: T-low = 0.1832 Scale= 0.276 R-factor= 0.7157 XSCLSQ: T-high= 0.1330 Scale= 0.840 R-factor= 0.3882 XSCLSQ: set 1 FOBS kscal= -1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 2 FCALC kscal= 1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 3 FBULK kscal= 0.869 bscal= 10.00 -0.131 9.97 XSCLSQ: ---------------------- Cycle 2 0.0010 ---------------------- XSCLSQ: Target= 0.3465 Scale= 0.685 R-factor= 0.4061 XSCLSQ: T-low = 0.1624 Scale= 0.416 R-factor= 0.6418 XSCLSQ: T-high= 0.1016 Scale= 0.905 R-factor= 0.3430 XSCLSQ: set 1 FOBS kscal= -1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 2 FCALC kscal= 1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 3 FBULK kscal= 0.723 bscal= 22.31 -0.146 12.31 XSCLSQ: ---------------------- Cycle 3 0.0001 ---------------------- XSCLSQ: Target= 0.2102 Scale= 0.854 R-factor= 0.3368 XSCLSQ: T-low = 0.1117 Scale= 0.691 R-factor= 0.4733 XSCLSQ: T-high= 0.0857 Scale= 0.926 R-factor= 0.3182 XSCLSQ: set 1 FOBS kscal= -1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 2 FCALC kscal= 1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 3 FBULK kscal= 0.581 bscal= 37.28 -0.142 14.97 XSCLSQ: ---------------------- Cycle 4 0.0000 ---------------------- XSCLSQ: Target= 0.1289 Scale= 0.931 R-factor= 0.3175 XSCLSQ: T-low = 0.0478 Scale= 0.953 R-factor= 0.3460 XSCLSQ: T-high= 0.0809 Scale= 0.924 R-factor= 0.3096 XSCLSQ: set 1 FOBS kscal= -1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 2 FCALC kscal= 1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 3 FBULK kscal= 0.456 bscal= 52.20 -0.125 14.92 XSCLSQ: ---------------------- Cycle 5 0.0000 ---------------------- XSCLSQ: Target= 0.1186 Scale= 0.930 R-factor= 0.3132 XSCLSQ: T-low = 0.0380 Scale= 0.961 R-factor= 0.3280 XSCLSQ: T-high= 0.0802 Scale= 0.920 R-factor= 0.3083 XSCLSQ: set 1 FOBS kscal= -1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 2 FCALC kscal= 1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 3 FBULK kscal= 0.409 bscal= 59.19 -0.046 6.98 XSCLSQ: ---------------------- Cycle 6 0.0000 ---------------------- XSCLSQ: Target= 0.1175 Scale= 0.926 R-factor= 0.3122 XSCLSQ: T-low = 0.0372 Scale= 0.950 R-factor= 0.3259 XSCLSQ: T-high= 0.0801 Scale= 0.918 R-factor= 0.3079 XSCLSQ: set 1 FOBS kscal= -1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 2 FCALC kscal= 1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 3 FBULK kscal= 0.399 bscal= 64.98 -0.011 5.79 XSCLSQ: ---------------------- Cycle 7 0.0000 ---------------------- XSCLSQ: Target= 0.1173 Scale= 0.924 R-factor= 0.3117 XSCLSQ: T-low = 0.0371 Scale= 0.943 R-factor= 0.3247 XSCLSQ: T-high= 0.0801 Scale= 0.917 R-factor= 0.3078 XSCLSQ: set 1 FOBS kscal= -1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 2 FCALC kscal= 1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 3 FBULK kscal= 0.393 bscal= 67.46 -0.006 2.48 XSCLSQ: ---------------------- Cycle 8 0.0000 ---------------------- XSCLSQ: Target= 0.1172 Scale= 0.923 R-factor= 0.3115 XSCLSQ: T-low = 0.0371 Scale= 0.940 R-factor= 0.3246 XSCLSQ: T-high= 0.0800 Scale= 0.917 R-factor= 0.3077 XSCLSQ: set 1 FOBS kscal= -1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 2 FCALC kscal= 1.000 bscal= 0.00 0.000 0.00 XSCLSQ: set 3 FBULK kscal= 0.392 bscal= 69.39 -0.001 1.92 XSCALE: ---------------------- Final ------------------------------------ XSCALE: Target= 0.1172 Scale= 0.923 R-factor= 0.3115 XSCALE: normal termination - convergence. MULTiscale: SET K B 1 FOBS -1.0000 0.0000 2 FCALC 1.0000 0.0000 3 FBULK 0.3920 69.3858 MULTiscale: K, B are stored in symbols $K, $B MULTiscale: the overall scale is stored in symbol $XSCFFK XSCALE: total number of data sets were selected 2 XSCALE: set 1 FOBS is specified as the target data set XSCLSQ: ---------------------- Cycle 0 0.0100 ---------------------- XSCLSQ: Target= 0.1095 Scale= 0.914 R-factor= 0.3059 XSCLSQ: set 1 FOBS kscal= -1.000 bscal_tensor= XSCLSQ: B11= 0.00 B22= 0.00 B33= 0.00 B12= 0.00 B13= 0.00 B23= 0.00 XSCLSQ: set 2 FBTOTA kscal= 1.000 bscal_tensor= XSCLSQ: B11= 0.00 B22= 0.00 B33= 0.00 B12= 0.00 B13= 0.00 B23= 0.00 XSCLSQ: ---------------------- Cycle 1 0.0100 ---------------------- XSCLSQ: Target= 0.1077 Scale= 0.917 R-factor= 0.3018 XSCLSQ: set 1 FOBS kscal= -1.000 bscal_tensor= XSCLSQ: B11= 0.00 B22= 0.00 B33= 0.00 B12= 0.00 B13= 0.00 B23= 0.00 XSCLSQ: set 2 FBTOTA kscal= 1.083 bscal_tensor= XSCLSQ: B11= 3.92 B22= 3.92 B33= 5.83 B12= 0.00 B13= 0.00 B23= 0.00 XSCLSQ: ---------------------- Cycle 2 0.0010 ---------------------- XSCLSQ: Target= 0.1077 Scale= 0.917 R-factor= 0.3017 XSCLSQ: set 1 FOBS kscal= -1.000 bscal_tensor= XSCLSQ: B11= 0.00 B22= 0.00 B33= 0.00 B12= 0.00 B13= 0.00 B23= 0.00 XSCLSQ: set 2 FBTOTA kscal= 1.089 bscal_tensor= XSCLSQ: B11= 4.20 B22= 4.20 B33= 6.22 B12= 0.00 B13= 0.00 B23= 0.00 XSCLSQ: ---------------------- Cycle 3 0.0001 ---------------------- XSCLSQ: Target= 0.1077 Scale= 0.917 R-factor= 0.3017 XSCLSQ: set 1 FOBS kscal= -1.000 bscal_tensor= XSCLSQ: B11= 0.00 B22= 0.00 B33= 0.00 B12= 0.00 B13= 0.00 B23= 0.00 XSCLSQ: set 2 FBTOTA kscal= 1.089 bscal_tensor= XSCLSQ: B11= 4.19 B22= 4.19 B33= 6.22 B12= 0.00 B13= 0.00 B23= 0.00 XSCALE: ---------------------- Final ------------------------------------ XSCALE: Target= 0.1077 Scale= 0.917 R-factor= 0.3017 XSCALE: normal termination - convergence. XSCALE: K has been multiplied by the overall scale ($XSCFFK) 0.917 MULTiscale: SET K B_tensor 1 FOBS -1.0000 B11= 0.000 B22= 0.000 B33= 0.000 B12= 0.000 B13= 0.000 B23= 0.000 2 FBTOTA 0.9986 B11= 4.193 B22= 4.193 B33= 6.216 B12= 0.000 B13= 0.000 B23= 0.000 MULTiscale: K is stored in symbols $K, and B_tensor MULTiscale: are stored in $B_11, $B_22, $B_33, etc. MULTiscale: the overall scale is stored in symbol $XSCFFK Trace/3 of the B-factor tensor has been subtraced from the B-factor atomic property array. The B-factor tensor has been modified to make the trace zero. modified tensor: B11= 0.674 B22= 0.674 B33= -1.348 B12= 0.000 B13= 0.000 B23= 0.000 SHOW: minimum of selected elements = 19.011964 CNSsolve> CNSsolve> xray XRAY> XRAY> tselection=(ref_active=1) XRAY> XRAY> @@CNS_XTALMODULE:refinementtarget (target=&reftarget; ASSFIL: file /sw/share/xtal/cns_solve_1.1/modules/xtal/refinementtarget opened. XRAY>! Module file: refinementtarget XRAY>! XRAY>! CNS module XRAY>! ********** XRAY>! XRAY>! Authors: Axel Brunger and Paul Adams XRAY>! XRAY>! copyright Yale University XRAY>! XRAY>! Function: XRAY>! Defines the crystallographic refinement targets XRAY>! XRAY>! Requirements: XRAY>! Needs to be called within xray XRAY> XRAY>module {refinementtarget} MODULE-DECLARATION> MODULE-DECLARATION>( MODULE-DECLARATION> &target="residual"; {string} MODULE-DECLARATION> &sig_sigacv=0.07; {real} MODULE-DECLARATION> &mbins=10; {real} MODULE-DECLARATION> &fobs=fobs; {reciprocal space array} MODULE-DECLARATION> &sigma=sigma; {reciprocal space array} MODULE-DECLARATION> &weight=weight; {reciprocal space array} MODULE-DECLARATION> &iobs=iobs; {reciprocal space array} MODULE-DECLARATION> &sigi=sigi; {reciprocal space array} MODULE-DECLARATION> &test=test; {reciprocal space array} MODULE-DECLARATION> &fcalc=fcalc; {reciprocal space array} MODULE-DECLARATION> &fpart=fpart; {reciprocal space array} MODULE-DECLARATION> &pa=pa; {reciprocal space array} MODULE-DECLARATION> &pb=pb; {reciprocal space array} MODULE-DECLARATION> &pc=pc; {reciprocal space array} MODULE-DECLARATION> &pd=pd; {reciprocal space array} MODULE-DECLARATION> &phase=phase; {reciprocal space array} MODULE-DECLARATION> &fom=fom; {reciprocal space array} MODULE-DECLARATION> &sel=all; {selection} MODULE-DECLARATION> &sel_test=none; {selection} MODULE-DECLARATION> &statistics=false; {logical} MODULE-DECLARATION>) &_2_TARGET set to &_1_REFTARGET MODULE-INVOCATION> sig_sigacv=0.07; &_2_SIG_SIGACV set to 0.07 MODULE-INVOCATION> mbins=&target_bins; &_2_MBINS set to &_1_TARGET_BINS MODULE-INVOCATION> fobs=&STRIP%obs_f; &_2_FOBS set to &STRIP%_1_OBS_F MODULE-INVOCATION> sigma=&STRIP%obs_sigf; &_2_SIGMA set to &STRIP%_1_OBS_SIGF MODULE-INVOCATION> weight=$STRIP%obs_w; &_2_WEIGHT set to $STRIP%_1_OBS_W MODULE-INVOCATION> iobs=$STRIP%obs_i; &_2_IOBS set to $STRIP%_1_OBS_I MODULE-INVOCATION> sigi=$STRIP%obs_sigi; &_2_SIGI set to $STRIP%_1_OBS_SIGI MODULE-INVOCATION> test=tst_active; &_2_TEST set to tst_active MODULE-INVOCATION> fcalc=fcalc; &_2_FCALC set to fcalc MODULE-INVOCATION> fpart=fbulk; &_2_FPART set to fbulk MODULE-INVOCATION> pa=&STRIP%obs_pa; &_2_PA set to &STRIP%_1_OBS_PA MODULE-INVOCATION> pb=&STRIP%obs_pb; &_2_PB set to &STRIP%_1_OBS_PB MODULE-INVOCATION> pc=&STRIP%obs_pc; &_2_PC set to &STRIP%_1_OBS_PC MODULE-INVOCATION> pd=&STRIP%obs_pd; &_2_PD set to &STRIP%_1_OBS_PD MODULE-INVOCATION> phase=&STRIP%obs_phase; &_2_PHASE set to &STRIP%_1_OBS_PHASE MODULE-INVOCATION> fom=&STRIP%obs_fom; &_2_FOM set to &STRIP%_1_OBS_FOM MODULE-INVOCATION> sel=(ref_active=1); &_2_SEL set to ( ref_active = 1 ) MODULE-INVOCATION> sel_test=(tst_active=1); &_2_SEL_TEST set to ( tst_active = 1 ) MODULE-INVOCATION> statistics=true;) &_2_STATISTICS set to true XRAY> XRAY>set message ? end MESSage=NORM XRAY>evaluate ($message_old=$result) EVALUATE: symbol $MESSAGE_OLD set to "NORM" (string) XRAY>set echo ? end ECHO=TRUE {ON} XRAY>evaluate ($echo_old=$result) EVALUATE: symbol $ECHO_OLD set to TRUE (logical) XRAY>if ( $log_level = verbose ) then NEXTCD: condition evaluated as false XRAY> set echo=on message=normal end XRAY>else XRAY> set echo=off message=off end Program version= 1.1 File version= 1.1 Sum of 959 elements = 959.0000 Sum of 959 elements = 959.0000 Sum of 9535 elements = 9535.0000 Sum of 0 elements = 0.0000 XSIGMAACV: Overall sigma for line restraint is 0.07000000 XSIGMAACV: step limit reached XSIGMAACV: Refinement of SIGMAA has finished Overall mean FOM is 0.71763 #bin | resolution range | #refl | 1 6.14 500.01 554 0.7651 182.9342 0.7387 0.9946 0.9941 2 4.87 6.14 558 0.8028 156.4155 0.7488 1.0000 1.0000 3 4.26 4.87 534 0.8362 177.7251 0.9560 0.9998 0.9993 4 3.87 4.26 540 0.7917 137.8019 0.7922 1.0000 1.0000 5 3.59 3.87 549 0.8434 110.9283 0.8063 0.9999 0.9994 6 3.38 3.59 525 0.8891 88.7955 1.0714 1.0000 1.0000 7 3.21 3.38 543 0.8666 85.3432 0.9212 0.9978 0.9975 8 3.07 3.21 521 0.7983 88.4219 0.8501 1.0000 1.0000 9 2.95 3.07 536 0.8010 89.2777 0.8947 1.0000 1.0000 10 2.85 2.95 517 0.7997 63.1924 0.8477 1.0000 1.0000 11 2.76 2.85 506 0.7663 63.2634 0.7962 1.0000 1.0000 12 2.68 2.76 511 0.7454 58.2681 0.7389 0.9958 0.9968 13 2.61 2.68 507 0.7692 60.3922 0.8309 1.0000 1.0000 14 2.55 2.61 500 0.7584 53.7012 0.8961 1.0000 1.0000 15 2.49 2.55 478 0.7868 42.4680 0.7687 1.0000 1.0000 16 2.44 2.49 476 0.7580 45.8784 0.8215 1.0000 1.0000 17 2.39 2.44 481 0.7188 47.4401 0.7307 0.9997 0.9998 18 2.34 2.39 469 0.7188 44.5816 0.6820 1.0000 1.0000 19 2.30 2.34 230 0.7621 41.0739 0.7064 1.0000 1.0000 #bin | resolution range | #refl | 1 6.14 500.01 54 0.3775 2 4.87 6.14 57 0.3990 3 4.26 4.87 46 0.3084 4 3.87 4.26 52 0.4179 5 3.59 3.87 52 0.2987 6 3.38 3.59 73 0.2855 7 3.21 3.38 52 0.2788 8 3.07 3.21 49 0.3965 9 2.95 3.07 48 0.3294 10 2.85 2.95 50 0.3273 11 2.76 2.85 59 0.3628 12 2.68 2.76 56 0.3762 13 2.61 2.68 55 0.3633 14 2.55 2.61 61 0.4010 15 2.49 2.55 41 0.2785 16 2.44 2.49 41 0.3773 17 2.39 2.44 48 0.3803 18 2.34 2.39 46 0.4190 19 2.30 2.34 19 0.2390 #bin | resolution range | #refl | 1 6.14 500.01 500 0.3416 2 4.87 6.14 501 0.2928 3 4.26 4.87 488 0.2646 4 3.87 4.26 488 0.2845 5 3.59 3.87 497 0.2985 6 3.38 3.59 452 0.3274 7 3.21 3.38 491 0.3107 8 3.07 3.21 472 0.3179 9 2.95 3.07 488 0.2967 10 2.85 2.95 467 0.3141 11 2.76 2.85 447 0.3251 12 2.68 2.76 455 0.3222 13 2.61 2.68 452 0.3200 14 2.55 2.61 439 0.2982 15 2.49 2.55 437 0.3198 16 2.44 2.49 435 0.3227 17 2.39 2.44 433 0.3258 18 2.34 2.39 423 0.3496 19 2.30 2.34 211 0.3284 XRAY> end CNSsolve> CNSsolve> if ( &anneal = true ) then NEXTCD: condition evaluated as true CNSsolve> CNSsolve> xray XRAY> tolerance=0.2 lookup=true XRAY> end CNSsolve> CNSsolve> do ( harm=0 ) ( all ) SELRPN: 1275 atoms have been selected out of 1275 CNSsolve> do ( harmonic=&k_harmonic ) ( &atom_harm ) SELRPN: 0 atoms have been selected out of 1275 CNSsolve> do ( harmonic=20 ) ( store9 or store8 ) SELRPN: 0 atoms have been selected out of 1275 CNSsolve> do ( refx=x ) ( all ) SELRPN: 1275 atoms have been selected out of 1275 CNSsolve> do ( refy=y ) ( all ) SELRPN: 1275 atoms have been selected out of 1275 CNSsolve> do ( refz=z ) ( all ) SELRPN: 1275 atoms have been selected out of 1275 CNSsolve> flags include harm end CNSsolve> CNSsolve> if ( &wa < 0 ) then NEXTCD: condition evaluated as true CNSsolve> @@CNS_XTALMODULE:getweight ( ASSFIL: file /sw/share/xtal/cns_solve_1.1/modules/xtal/getweight opened. CNSsolve>! Module file: getweight CNSsolve>! CNSsolve>! CNS module CNSsolve>! ********** CNSsolve>! CNSsolve>! Authors: Axel T. Brunger and Paul Adams CNSsolve>! CNSsolve>! copyright Yale University CNSsolve>! CNSsolve>! Function: CNSsolve>! Calculate the weight for the crystallographic energy term CNSsolve>! CNSsolve>! Requirements: CNSsolve>! To be called from the main level CNSsolve>! Uses comparision coordinate set and also vx, vy, vz CNSsolve>! This module uses store5 CNSsolve> CNSsolve>module {getweight} MODULE-DECLARATION>( MODULE-DECLARATION> &selected=(all); MODULE-DECLARATION> &fixed=(none); MODULE-DECLARATION> &wa=$wa_temp; MODULE-DECLARATION>) MODULE-INVOCATION> selected=&atom_select; &_2_SELECTED set to &_1_ATOM_SELECT MODULE-INVOCATION> fixed=(store7); &_2_FIXED set to ( store7 ) MODULE-INVOCATION> ) CNSsolve> CNSsolve>set message ? end MESSage=NORM CNSsolve>evaluate ($message_old=$result) EVALUATE: symbol $MESSAGE_OLD set to "NORM" (string) CNSsolve>set echo ? end ECHO=TRUE {ON} CNSsolve>evaluate ($echo_old=$result) EVALUATE: symbol $ECHO_OLD set to TRUE (logical) CNSsolve>if ( $log_level = verbose ) then NEXTCD: condition evaluated as false CNSsolve> set echo=on message=normal end CNSsolve>else CNSsolve> set echo=off message=off end Program version= 1.1 File version= 1.1 SEED= 82364. POWELL: number of degrees of freedom= 3657 NBONDS: generating intra-molecular exclusion list with mode= 5 MAKINB: mode 5 found 2914 exclusions and 1876 interactions(1-4) NBONDS: found 30679 intra-atom interactions NBONDS: found 2910 symmetry-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =1021.589 grad(E)=10.400 E(BOND)=25.375 E(ANGL)=154.936 | | E(DIHE)=571.907 E(IMPR)=40.175 E(VDW )=219.036 E(PVDW)=10.161 | | E(HARM)=0.000 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum DCART: velocity rescaling (VSCAling) enabled CENMAS: Information about center of free masses position [A] : -15.86151 13.42637 -1.69020 velocity [A/ps] : -0.05558 -0.07721 -0.10985 ang. mom. [amu A/ps] : -44495.78966 -16168.52397 11784.36632 kin. ener. [Kcal/mol] : 0.43103 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -15.86151 13.42637 -1.69020 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 -------------------------- Cartesian dynamics start --------------------------- | E(kin)+E(total)=2111.662 E(kin)=1090.074 temperature=300.000 | | Etotal =1021.589 grad(E)=10.400 E(BOND)=25.375 E(ANGL)=154.936 | | E(DIHE)=571.907 E(IMPR)=40.175 E(VDW )=219.036 E(PVDW)=10.161 | | E(HARM)=0.000 | ------------------------------------------------------------------------------- NBONDS: found 30655 intra-atom interactions NBONDS: found 2912 symmetry-atom interactions NBONDS: found 30680 intra-atom interactions NBONDS: found 2889 symmetry-atom interactions NBONDS: found 30659 intra-atom interactions NBONDS: found 2884 symmetry-atom interactions NBONDS: found 30656 intra-atom interactions NBONDS: found 2866 symmetry-atom interactions -------------------- final step= 200 at 0.10000 ps --------------------- | E(kin)+E(total)=2496.370 E(kin)=1090.074 temperature=300.000 | | Etotal =1406.297 grad(E)=38.730 E(BOND)=237.931 E(ANGL)=364.743 | | E(DIHE)=392.478 E(IMPR)=121.704 E(VDW )=280.147 E(PVDW)=9.294 | | E(HARM)=0.000 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : -15.86296 13.42105 -1.68918 velocity [A/ps] : -0.02626 -0.09627 0.02533 ang. mom. [amu A/ps] : -3872.16986 47333.01277 -9633.72170 kin. ener. [Kcal/mol] : 0.21636 --------------- cycle= 1 -------------------------------------------------- | Etotal =1406.297 grad(E)=38.730 E(BOND)=237.931 E(ANGL)=364.743 | | E(DIHE)=392.478 E(IMPR)=121.704 E(VDW )=280.147 E(PVDW)=9.294 | | E(HARM)=0.000 | ------------------------------------------------------------------------------- SHOW: sum over selected elements = 1219.000000 SHOW: sum over selected elements = 5735967.377657 --------------- cycle= 2 -------------------------------------------------- | Etotal =38992.153 grad(E)=39.181 E(BOND)=237.931 E(ANGL)=364.743 | | E(DIHE)=392.478 E(IMPR)=121.704 E(VDW )=280.147 E(PVDW)=9.294 | | E(HARM)=0.000 E(XREF)=37585.856 | ------------------------------------------------------------------------------- SHOW: rms deviation from aver of selected elements = 151.764809 SHOW: rms deviation from aver of selected elements = 76.529855 SHOW: sum over selected elements = 102555.872966 getweight: optimal weight= 3.73932 CNSsolve> end if CNSsolve> CNSsolve> parameter PARRDR> nbonds NBDSET> repel ? evaluate ($repel_old=$result) REPEl-factor= 1.0000 EVALUATE: symbol $REPEL_OLD set to 1.00000 (real) NBDSET> rcon ? evaluate ($rcon_old=$result) RCONstant= 16.000 EVALUATE: symbol $RCON_OLD set to 16.0000 (real) NBDSET> if ($repel_old =1 ) then NEXTCD: condition evaluated as true NBDSET> repel=1. rcon=100. NBDSET> else NBDSET> repel=.75 rcon=50. NBDSET> end if NBDSET> end PARRDR> end CNSsolve> CNSsolve> do (fbeta=$fbeta) ( ( &atom_select ) and not (store7) ) SELRPN: 1219 atoms have been selected out of 1275 CNSsolve> CNSsolve> do (vx=maxwell($start_temp)) (&atom_select and not (store7)) SELRPN: 1219 atoms have been selected out of 1275 CNSsolve> do (vy=maxwell($start_temp)) (&atom_select and not (store7)) SELRPN: 1219 atoms have been selected out of 1275 CNSsolve> do (vz=maxwell($start_temp)) (&atom_select and not (store7)) SELRPN: 1219 atoms have been selected out of 1275 CNSsolve> CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> topology Torsion Topology> Torsion Topology> maxlength=&torsion_maxlength Torsion Topology> maxchain=&torsion_maxchain Torsion Topology> maxtree=&torsion_maxtree Torsion Topology> maxbond=&torsion_maxbond Torsion Topology> kdihmax = 95. Torsion Topology> Torsion Topology> @CNS_TOPPAR:torsionmdmods ASSFIL: file /sw/share/xtal/cns_solve_1.1/libraries/toppar/torsionmdmods opened. Torsion Topology>! CNS toppar file: torsionmdmods Torsion Topology>! Torsion Topology>! Authors: Axel Brunger and Luke Rice Torsion Topology>! Torsion Topology>! copyright Yale University Torsion Topology>! Torsion Topology>! Function: Torsion Topology>! Applies various patches to torsion angle dynamics Torsion Topology>! necessary for certain topologies Torsion Topology>! Torsion Topology>! Requirements: Torsion Topology>! Needs to be called from torsion topology Torsion Topology> Torsion Topology> Torsion Topology>set message ? end MESSage=NORM Torsion Topology>evaluate ($message_old_tmod=$result) EVALUATE: symbol $MESSAGE_OLD_TMOD set to "NORM" (string) Torsion Topology>set echo ? end ECHO=TRUE {ON} Torsion Topology>evaluate ($echo_old_tmod=$result) EVALUATE: symbol $ECHO_OLD_TMOD set to TRUE (logical) Torsion Topology>if ( $log_level = verbose ) then NEXTCD: condition evaluated as false Torsion Topology> set echo=on message=normal end Torsion Topology>else Torsion Topology> set echo=off message=off end Program version= 1.1 File version= 1.1 Torsion Topology> Torsion Topology> fix group ( &atom_rigid ) SELRPN: 0 atoms have been selected out of 1275 Torsion Topology> Torsion Topology> end Torsion Dynamics> nstep=0 Torsion Dynamics> cmremove=true Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Current Velocities Taken Bad Initial Velocities May Result ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : -15.85725 13.42649 -1.69224 velocity [A/ps] : 101.70699 -194.59689 32.58280 ang. mom. [amu A/ps] :6769160.31877 329083.43060************* kin. ener. [Kcal/mol] :1006836.88335 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -15.85725 13.42649 -1.69224 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 CNSsolve> end if CNSsolve> CNSsolve> do (store6=mass) ( all ) SELRPN: 1275 atoms have been selected out of 1275 CNSsolve> do (mass=max(10,min(30,mass))) ( all ) SELRPN: 1275 atoms have been selected out of 1275 CNSsolve> CNSsolve> evaluate ( $curr_temp = &temperature ) EVALUATE: symbol $CURR_TEMP set to 1000.00 (real) CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- NBONDS: generating intra-molecular exclusion list with mode= 5 MAKINB: mode 5 found 2914 exclusions and 1876 interactions(1-4) NBONDS: found 30679 intra-atom interactions NBONDS: found 2910 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.349 XTAREXPR: ->[WORKING SET] monitor= 0.306 TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140142.321 E(kin)=595.164 temperature=1000.000 | | Etotal =139547.157 grad(E)=37.385 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=752.917 E(IMPR)=111.092 E(VDW )=1569.775 E(PVDW)=63.727 | | E(HARM)=0.000 E(XREF)=136306.086 | ------------------------------------------------------------------------------- ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140054.325 E(kin)=595.164 temperature=1000.000 | | Etotal =139459.161 grad(E)=37.323 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=754.463 E(IMPR)=111.092 E(VDW )=1542.647 E(PVDW)=53.115 | | E(HARM)=0.000 E(XREF)=136254.283 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.346 XTAREXPR: ->[WORKING SET] monitor= 0.313 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 975.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140424.310 E(kin)=580.285 temperature=975.000 | | Etotal =139844.025 grad(E)=37.516 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=755.422 E(IMPR)=111.092 E(VDW )=1544.713 E(PVDW)=51.879 | | E(HARM)=0.000 E(XREF)=136637.359 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.346 XTAREXPR: ->[WORKING SET] monitor= 0.320 NBONDS: found 30594 intra-atom interactions NBONDS: found 2879 symmetry-atom interactions ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140884.486 E(kin)=580.285 temperature=975.000 | | Etotal =140304.202 grad(E)=37.852 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=759.891 E(IMPR)=111.092 E(VDW )=1550.570 E(PVDW)=49.395 | | E(HARM)=0.000 E(XREF)=137089.693 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 950.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140870.311 E(kin)=565.406 temperature=950.000 | | Etotal =140304.905 grad(E)=37.821 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=760.243 E(IMPR)=111.092 E(VDW )=1548.089 E(PVDW)=50.392 | | E(HARM)=0.000 E(XREF)=137091.529 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.347 XTAREXPR: ->[WORKING SET] monitor= 0.325 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.348 XTAREXPR: ->[WORKING SET] monitor= 0.326 NBONDS: found 30512 intra-atom interactions NBONDS: found 2843 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.349 XTAREXPR: ->[WORKING SET] monitor= 0.325 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140943.697 E(kin)=565.406 temperature=950.000 | | Etotal =140378.291 grad(E)=37.743 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=757.572 E(IMPR)=111.092 E(VDW )=1580.630 E(PVDW)=57.843 | | E(HARM)=0.000 E(XREF)=137127.593 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 925.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140903.281 E(kin)=550.526 temperature=925.000 | | Etotal =140352.755 grad(E)=37.798 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=755.676 E(IMPR)=111.092 E(VDW )=1593.324 E(PVDW)=57.621 | | E(HARM)=0.000 E(XREF)=137091.481 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.351 XTAREXPR: ->[WORKING SET] monitor= 0.325 NBONDS: found 30531 intra-atom interactions NBONDS: found 2830 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.323 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140791.033 E(kin)=550.526 temperature=925.000 | | Etotal =140240.506 grad(E)=37.930 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=741.904 E(IMPR)=111.092 E(VDW )=1636.749 E(PVDW)=49.637 | | E(HARM)=0.000 E(XREF)=136957.563 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 900.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140699.593 E(kin)=535.647 temperature=900.000 | | Etotal =140163.945 grad(E)=37.914 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=740.362 E(IMPR)=111.092 E(VDW )=1635.894 E(PVDW)=48.244 | | E(HARM)=0.000 E(XREF)=136884.792 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.320 NBONDS: found 30601 intra-atom interactions NBONDS: found 2821 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.318 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140507.192 E(kin)=535.647 temperature=900.000 | | Etotal =139971.545 grad(E)=37.639 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=748.391 E(IMPR)=111.092 E(VDW )=1566.890 E(PVDW)=46.799 | | E(HARM)=0.000 E(XREF)=136754.812 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 875.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140439.486 E(kin)=520.768 temperature=875.000 | | Etotal =139918.718 grad(E)=37.585 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=752.137 E(IMPR)=111.092 E(VDW )=1552.002 E(PVDW)=47.758 | | E(HARM)=0.000 E(XREF)=136712.169 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.316 NBONDS: found 30636 intra-atom interactions NBONDS: found 2847 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.353 XTAREXPR: ->[WORKING SET] monitor= 0.316 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140391.454 E(kin)=520.768 temperature=875.000 | | Etotal =139870.686 grad(E)=37.531 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=769.129 E(IMPR)=111.092 E(VDW )=1519.635 E(PVDW)=54.599 | | E(HARM)=0.000 E(XREF)=136672.671 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 850.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140324.425 E(kin)=505.889 temperature=850.000 | | Etotal =139818.536 grad(E)=37.548 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=771.205 E(IMPR)=111.092 E(VDW )=1524.249 E(PVDW)=56.978 | | E(HARM)=0.000 E(XREF)=136611.451 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.355 XTAREXPR: ->[WORKING SET] monitor= 0.315 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.355 XTAREXPR: ->[WORKING SET] monitor= 0.314 NBONDS: found 30700 intra-atom interactions NBONDS: found 2903 symmetry-atom interactions ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140307.643 E(kin)=505.889 temperature=850.000 | | Etotal =139801.754 grad(E)=37.826 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=773.550 E(IMPR)=111.092 E(VDW )=1574.922 E(PVDW)=68.017 | | E(HARM)=0.000 E(XREF)=136530.613 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.355 XTAREXPR: ->[WORKING SET] monitor= 0.313 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 825.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140325.032 E(kin)=491.010 temperature=825.000 | | Etotal =139834.022 grad(E)=37.749 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=772.717 E(IMPR)=111.092 E(VDW )=1577.308 E(PVDW)=67.801 | | E(HARM)=0.000 E(XREF)=136561.543 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.355 XTAREXPR: ->[WORKING SET] monitor= 0.313 NBONDS: found 30724 intra-atom interactions NBONDS: found 2893 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.355 XTAREXPR: ->[WORKING SET] monitor= 0.314 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140425.361 E(kin)=491.010 temperature=825.000 | | Etotal =139934.351 grad(E)=37.968 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=765.724 E(IMPR)=111.092 E(VDW )=1597.854 E(PVDW)=56.603 | | E(HARM)=0.000 E(XREF)=136659.517 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 800.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140429.703 E(kin)=476.131 temperature=800.000 | | Etotal =139953.572 grad(E)=38.049 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=765.551 E(IMPR)=111.092 E(VDW )=1609.706 E(PVDW)=54.278 | | E(HARM)=0.000 E(XREF)=136669.384 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.355 XTAREXPR: ->[WORKING SET] monitor= 0.315 NBONDS: found 30714 intra-atom interactions NBONDS: found 2892 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.356 XTAREXPR: ->[WORKING SET] monitor= 0.315 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140381.264 E(kin)=476.131 temperature=800.000 | | Etotal =139905.133 grad(E)=37.793 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=775.790 E(IMPR)=111.092 E(VDW )=1592.577 E(PVDW)=54.504 | | E(HARM)=0.000 E(XREF)=136627.610 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.355 XTAREXPR: ->[WORKING SET] monitor= 0.314 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 775.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140376.309 E(kin)=461.252 temperature=775.000 | | Etotal =139915.057 grad(E)=37.688 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=777.342 E(IMPR)=111.092 E(VDW )=1583.050 E(PVDW)=57.027 | | E(HARM)=0.000 E(XREF)=136642.985 | ------------------------------------------------------------------------------- NBONDS: found 30692 intra-atom interactions NBONDS: found 2912 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.355 XTAREXPR: ->[WORKING SET] monitor= 0.313 NBONDS: found 30719 intra-atom interactions NBONDS: found 2926 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.355 XTAREXPR: ->[WORKING SET] monitor= 0.314 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140284.894 E(kin)=461.252 temperature=775.000 | | Etotal =139823.642 grad(E)=37.512 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=775.956 E(IMPR)=111.092 E(VDW )=1536.101 E(PVDW)=66.418 | | E(HARM)=0.000 E(XREF)=136590.514 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 750.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140211.572 E(kin)=446.373 temperature=750.000 | | Etotal =139765.199 grad(E)=37.472 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=774.070 E(IMPR)=111.092 E(VDW )=1532.326 E(PVDW)=65.661 | | E(HARM)=0.000 E(XREF)=136538.489 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.354 XTAREXPR: ->[WORKING SET] monitor= 0.315 NBONDS: found 30709 intra-atom interactions NBONDS: found 2919 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.315 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.351 XTAREXPR: ->[WORKING SET] monitor= 0.315 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140303.565 E(kin)=446.373 temperature=750.000 | | Etotal =139857.193 grad(E)=37.756 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=761.809 E(IMPR)=111.092 E(VDW )=1555.443 E(PVDW)=57.601 | | E(HARM)=0.000 E(XREF)=136627.687 | ------------------------------------------------------------------------------- NBONDS: found 30731 intra-atom interactions NBONDS: found 2904 symmetry-atom interactions CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 725.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140264.147 E(kin)=431.494 temperature=725.000 | | Etotal =139832.653 grad(E)=37.830 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=758.350 E(IMPR)=111.092 E(VDW )=1568.834 E(PVDW)=55.797 | | E(HARM)=0.000 E(XREF)=136595.019 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.314 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.313 NBONDS: found 30734 intra-atom interactions NBONDS: found 2896 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.313 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140244.048 E(kin)=431.494 temperature=725.000 | | Etotal =139812.555 grad(E)=38.082 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=739.323 E(IMPR)=111.092 E(VDW )=1599.073 E(PVDW)=48.274 | | E(HARM)=0.000 E(XREF)=136571.231 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 700.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140193.757 E(kin)=416.615 temperature=700.000 | | Etotal =139777.142 grad(E)=38.027 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=737.805 E(IMPR)=111.092 E(VDW )=1589.914 E(PVDW)=48.106 | | E(HARM)=0.000 E(XREF)=136546.665 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.351 XTAREXPR: ->[WORKING SET] monitor= 0.312 NBONDS: found 30744 intra-atom interactions NBONDS: found 2885 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.353 XTAREXPR: ->[WORKING SET] monitor= 0.312 NBONDS: found 30740 intra-atom interactions NBONDS: found 2891 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.354 XTAREXPR: ->[WORKING SET] monitor= 0.313 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140309.122 E(kin)=416.615 temperature=700.000 | | Etotal =139892.507 grad(E)=38.048 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=746.879 E(IMPR)=111.092 E(VDW )=1594.935 E(PVDW)=56.380 | | E(HARM)=0.000 E(XREF)=136639.661 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 675.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140296.548 E(kin)=401.736 temperature=675.000 | | Etotal =139894.813 grad(E)=38.066 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=749.368 E(IMPR)=111.092 E(VDW )=1596.491 E(PVDW)=59.131 | | E(HARM)=0.000 E(XREF)=136635.169 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.354 XTAREXPR: ->[WORKING SET] monitor= 0.313 NBONDS: found 30682 intra-atom interactions NBONDS: found 2907 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.354 XTAREXPR: ->[WORKING SET] monitor= 0.313 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.353 XTAREXPR: ->[WORKING SET] monitor= 0.313 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140156.695 E(kin)=401.736 temperature=675.000 | | Etotal =139754.960 grad(E)=37.587 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=759.922 E(IMPR)=111.092 E(VDW )=1529.345 E(PVDW)=54.178 | | E(HARM)=0.000 E(XREF)=136556.862 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 650.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140112.749 E(kin)=386.856 temperature=650.000 | | Etotal =139725.893 grad(E)=37.590 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=760.671 E(IMPR)=111.092 E(VDW )=1524.580 E(PVDW)=53.440 | | E(HARM)=0.000 E(XREF)=136532.548 | ------------------------------------------------------------------------------- NBONDS: found 30648 intra-atom interactions NBONDS: found 2919 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.353 XTAREXPR: ->[WORKING SET] monitor= 0.314 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.354 XTAREXPR: ->[WORKING SET] monitor= 0.315 NBONDS: found 30648 intra-atom interactions NBONDS: found 2917 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.355 XTAREXPR: ->[WORKING SET] monitor= 0.315 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140228.333 E(kin)=386.856 temperature=650.000 | | Etotal =139841.477 grad(E)=38.182 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=757.941 E(IMPR)=111.092 E(VDW )=1583.036 E(PVDW)=67.458 | | E(HARM)=0.000 E(XREF)=136578.389 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 625.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140204.183 E(kin)=371.977 temperature=625.000 | | Etotal =139832.205 grad(E)=38.289 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=758.728 E(IMPR)=111.092 E(VDW )=1597.803 E(PVDW)=68.953 | | E(HARM)=0.000 E(XREF)=136552.069 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.356 XTAREXPR: ->[WORKING SET] monitor= 0.315 NBONDS: found 30653 intra-atom interactions NBONDS: found 2909 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.357 XTAREXPR: ->[WORKING SET] monitor= 0.313 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.358 XTAREXPR: ->[WORKING SET] monitor= 0.312 NBONDS: found 30707 intra-atom interactions NBONDS: found 2899 symmetry-atom interactions ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140091.587 E(kin)=371.977 temperature=625.000 | | Etotal =139719.610 grad(E)=37.522 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=763.334 E(IMPR)=111.092 E(VDW )=1559.056 E(PVDW)=57.664 | | E(HARM)=0.000 E(XREF)=136484.903 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 600.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140055.723 E(kin)=357.098 temperature=600.000 | | Etotal =139698.625 grad(E)=37.510 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=763.311 E(IMPR)=111.092 E(VDW )=1564.970 E(PVDW)=57.501 | | E(HARM)=0.000 E(XREF)=136458.190 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.359 XTAREXPR: ->[WORKING SET] monitor= 0.312 NBONDS: found 30727 intra-atom interactions NBONDS: found 2902 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.359 XTAREXPR: ->[WORKING SET] monitor= 0.311 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.358 XTAREXPR: ->[WORKING SET] monitor= 0.311 NBONDS: found 30746 intra-atom interactions NBONDS: found 2907 symmetry-atom interactions ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140104.207 E(kin)=357.098 temperature=600.000 | | Etotal =139747.108 grad(E)=37.942 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=760.233 E(IMPR)=111.092 E(VDW )=1580.387 E(PVDW)=60.478 | | E(HARM)=0.000 E(XREF)=136491.357 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.357 XTAREXPR: ->[WORKING SET] monitor= 0.310 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 575.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140059.297 E(kin)=342.219 temperature=575.000 | | Etotal =139717.078 grad(E)=37.661 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=761.433 E(IMPR)=111.092 E(VDW )=1562.937 E(PVDW)=58.871 | | E(HARM)=0.000 E(XREF)=136479.184 | ------------------------------------------------------------------------------- NBONDS: found 30728 intra-atom interactions NBONDS: found 2909 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.354 XTAREXPR: ->[WORKING SET] monitor= 0.310 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.353 XTAREXPR: ->[WORKING SET] monitor= 0.311 NBONDS: found 30739 intra-atom interactions NBONDS: found 2921 symmetry-atom interactions ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139990.450 E(kin)=342.219 temperature=575.000 | | Etotal =139648.231 grad(E)=37.478 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=760.004 E(IMPR)=111.092 E(VDW )=1551.046 E(PVDW)=55.526 | | E(HARM)=0.000 E(XREF)=136427.002 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.312 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 550.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140046.442 E(kin)=327.340 temperature=550.000 | | Etotal =139719.102 grad(E)=37.666 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=757.824 E(IMPR)=111.092 E(VDW )=1555.736 E(PVDW)=56.190 | | E(HARM)=0.000 E(XREF)=136494.699 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.313 NBONDS: found 30737 intra-atom interactions NBONDS: found 2931 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.314 NBONDS: found 30728 intra-atom interactions NBONDS: found 2932 symmetry-atom interactions ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140059.120 E(kin)=327.340 temperature=550.000 | | Etotal =139731.780 grad(E)=37.922 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=741.339 E(IMPR)=111.092 E(VDW )=1572.612 E(PVDW)=61.155 | | E(HARM)=0.000 E(XREF)=136502.022 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.353 XTAREXPR: ->[WORKING SET] monitor= 0.313 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 525.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140048.514 E(kin)=312.461 temperature=525.000 | | Etotal =139736.053 grad(E)=37.796 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=740.537 E(IMPR)=111.092 E(VDW )=1566.963 E(PVDW)=62.494 | | E(HARM)=0.000 E(XREF)=136511.405 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.353 XTAREXPR: ->[WORKING SET] monitor= 0.313 NBONDS: found 30738 intra-atom interactions NBONDS: found 2926 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.353 XTAREXPR: ->[WORKING SET] monitor= 0.313 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.312 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=140033.162 E(kin)=312.461 temperature=525.000 | | Etotal =139720.701 grad(E)=37.758 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=749.671 E(IMPR)=111.092 E(VDW )=1543.389 E(PVDW)=65.234 | | E(HARM)=0.000 E(XREF)=136507.755 | ------------------------------------------------------------------------------- NBONDS: found 30738 intra-atom interactions NBONDS: found 2926 symmetry-atom interactions CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 500.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=140015.500 E(kin)=297.582 temperature=500.000 | | Etotal =139717.918 grad(E)=37.769 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=751.081 E(IMPR)=111.092 E(VDW )=1540.566 E(PVDW)=62.823 | | E(HARM)=0.000 E(XREF)=136508.795 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.353 XTAREXPR: ->[WORKING SET] monitor= 0.312 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.311 NBONDS: found 30757 intra-atom interactions NBONDS: found 2912 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.311 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139948.602 E(kin)=297.582 temperature=500.000 | | Etotal =139651.020 grad(E)=37.471 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=749.200 E(IMPR)=111.092 E(VDW )=1518.735 E(PVDW)=50.457 | | E(HARM)=0.000 E(XREF)=136477.976 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.351 XTAREXPR: ->[WORKING SET] monitor= 0.311 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 475.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139926.144 E(kin)=282.703 temperature=475.000 | | Etotal =139643.441 grad(E)=37.427 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=749.775 E(IMPR)=111.092 E(VDW )=1525.130 E(PVDW)=49.589 | | E(HARM)=0.000 E(XREF)=136464.294 | ------------------------------------------------------------------------------- NBONDS: found 30715 intra-atom interactions NBONDS: found 2907 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.311 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.349 XTAREXPR: ->[WORKING SET] monitor= 0.311 NBONDS: found 30696 intra-atom interactions NBONDS: found 2925 symmetry-atom interactions ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139957.309 E(kin)=282.703 temperature=475.000 | | Etotal =139674.606 grad(E)=37.738 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=754.490 E(IMPR)=111.092 E(VDW )=1581.442 E(PVDW)=52.457 | | E(HARM)=0.000 E(XREF)=136431.565 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.349 XTAREXPR: ->[WORKING SET] monitor= 0.312 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 450.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139965.723 E(kin)=267.824 temperature=450.000 | | Etotal =139697.899 grad(E)=37.790 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=753.441 E(IMPR)=111.092 E(VDW )=1585.372 E(PVDW)=54.349 | | E(HARM)=0.000 E(XREF)=136450.085 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.312 NBONDS: found 30687 intra-atom interactions NBONDS: found 2930 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.312 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139910.917 E(kin)=267.824 temperature=450.000 | | Etotal =139643.093 grad(E)=37.692 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=740.476 E(IMPR)=111.092 E(VDW )=1570.164 E(PVDW)=68.876 | | E(HARM)=0.000 E(XREF)=136408.925 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.312 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 425.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139897.777 E(kin)=252.945 temperature=425.000 | | Etotal =139644.832 grad(E)=37.634 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=738.731 E(IMPR)=111.092 E(VDW )=1562.680 E(PVDW)=69.589 | | E(HARM)=0.000 E(XREF)=136419.179 | ------------------------------------------------------------------------------- NBONDS: found 30688 intra-atom interactions NBONDS: found 2927 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.312 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.312 NBONDS: found 30693 intra-atom interactions NBONDS: found 2924 symmetry-atom interactions ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139882.250 E(kin)=252.945 temperature=425.000 | | Etotal =139629.305 grad(E)=37.678 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=736.829 E(IMPR)=111.092 E(VDW )=1528.483 E(PVDW)=57.758 | | E(HARM)=0.000 E(XREF)=136451.582 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.312 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 400.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139865.591 E(kin)=238.065 temperature=400.000 | | Etotal =139627.525 grad(E)=37.585 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=735.663 E(IMPR)=111.092 E(VDW )=1510.906 E(PVDW)=56.558 | | E(HARM)=0.000 E(XREF)=136469.745 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.353 XTAREXPR: ->[WORKING SET] monitor= 0.312 NBONDS: found 30727 intra-atom interactions NBONDS: found 2913 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.354 XTAREXPR: ->[WORKING SET] monitor= 0.311 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.354 XTAREXPR: ->[WORKING SET] monitor= 0.311 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139856.075 E(kin)=238.065 temperature=400.000 | | Etotal =139618.010 grad(E)=37.584 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=731.657 E(IMPR)=111.092 E(VDW )=1523.265 E(PVDW)=54.099 | | E(HARM)=0.000 E(XREF)=136454.336 | ------------------------------------------------------------------------------- NBONDS: found 30741 intra-atom interactions NBONDS: found 2903 symmetry-atom interactions CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 375.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139825.204 E(kin)=223.186 temperature=375.000 | | Etotal =139602.017 grad(E)=37.603 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=734.088 E(IMPR)=111.092 E(VDW )=1532.821 E(PVDW)=52.964 | | E(HARM)=0.000 E(XREF)=136427.491 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.353 XTAREXPR: ->[WORKING SET] monitor= 0.311 NBONDS: found 30722 intra-atom interactions NBONDS: found 2904 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.311 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.351 XTAREXPR: ->[WORKING SET] monitor= 0.311 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139840.767 E(kin)=223.186 temperature=375.000 | | Etotal =139617.581 grad(E)=37.488 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=752.957 E(IMPR)=111.092 E(VDW )=1550.701 E(PVDW)=53.946 | | E(HARM)=0.000 E(XREF)=136405.324 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 350.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139827.921 E(kin)=208.307 temperature=350.000 | | Etotal =139619.614 grad(E)=37.530 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=755.219 E(IMPR)=111.092 E(VDW )=1556.591 E(PVDW)=55.731 | | E(HARM)=0.000 E(XREF)=136397.421 | ------------------------------------------------------------------------------- NBONDS: found 30736 intra-atom interactions NBONDS: found 2914 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.311 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.349 XTAREXPR: ->[WORKING SET] monitor= 0.311 NBONDS: found 30732 intra-atom interactions NBONDS: found 2919 symmetry-atom interactions ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139796.780 E(kin)=208.307 temperature=350.000 | | Etotal =139588.472 grad(E)=37.792 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=751.287 E(IMPR)=111.092 E(VDW )=1575.817 E(PVDW)=62.346 | | E(HARM)=0.000 E(XREF)=136344.369 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.349 XTAREXPR: ->[WORKING SET] monitor= 0.310 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 325.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139796.635 E(kin)=193.428 temperature=325.000 | | Etotal =139603.207 grad(E)=37.874 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=749.002 E(IMPR)=111.092 E(VDW )=1584.282 E(PVDW)=62.424 | | E(HARM)=0.000 E(XREF)=136352.846 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.349 XTAREXPR: ->[WORKING SET] monitor= 0.310 NBONDS: found 30698 intra-atom interactions NBONDS: found 2909 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.310 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139695.314 E(kin)=193.428 temperature=325.000 | | Etotal =139501.886 grad(E)=37.420 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=739.637 E(IMPR)=111.092 E(VDW )=1517.984 E(PVDW)=60.927 | | E(HARM)=0.000 E(XREF)=136328.686 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.310 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 300.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139721.728 E(kin)=178.549 temperature=300.000 | | Etotal =139543.179 grad(E)=37.447 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=736.986 E(IMPR)=111.092 E(VDW )=1514.558 E(PVDW)=60.328 | | E(HARM)=0.000 E(XREF)=136376.654 | ------------------------------------------------------------------------------- NBONDS: found 30697 intra-atom interactions NBONDS: found 2919 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.354 XTAREXPR: ->[WORKING SET] monitor= 0.311 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.355 XTAREXPR: ->[WORKING SET] monitor= 0.311 NBONDS: found 30692 intra-atom interactions NBONDS: found 2931 symmetry-atom interactions ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139754.584 E(kin)=178.549 temperature=300.000 | | Etotal =139576.035 grad(E)=37.478 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=727.893 E(IMPR)=111.092 E(VDW )=1528.073 E(PVDW)=55.831 | | E(HARM)=0.000 E(XREF)=136409.585 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.355 XTAREXPR: ->[WORKING SET] monitor= 0.311 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 275.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139737.604 E(kin)=163.670 temperature=275.000 | | Etotal =139573.934 grad(E)=37.370 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=730.159 E(IMPR)=111.092 E(VDW )=1524.352 E(PVDW)=54.105 | | E(HARM)=0.000 E(XREF)=136410.665 | ------------------------------------------------------------------------------- NBONDS: found 30690 intra-atom interactions NBONDS: found 2927 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.354 XTAREXPR: ->[WORKING SET] monitor= 0.310 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.353 XTAREXPR: ->[WORKING SET] monitor= 0.310 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139738.229 E(kin)=163.670 temperature=275.000 | | Etotal =139574.559 grad(E)=37.464 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=745.362 E(IMPR)=111.092 E(VDW )=1542.347 E(PVDW)=50.727 | | E(HARM)=0.000 E(XREF)=136381.470 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 250.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139720.218 E(kin)=148.791 temperature=250.000 | | Etotal =139571.427 grad(E)=37.504 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=746.672 E(IMPR)=111.092 E(VDW )=1547.621 E(PVDW)=51.878 | | E(HARM)=0.000 E(XREF)=136370.603 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.310 NBONDS: found 30706 intra-atom interactions NBONDS: found 2919 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.351 XTAREXPR: ->[WORKING SET] monitor= 0.310 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139630.039 E(kin)=148.791 temperature=250.000 | | Etotal =139481.248 grad(E)=37.678 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=741.571 E(IMPR)=111.092 E(VDW )=1562.032 E(PVDW)=58.204 | | E(HARM)=0.000 E(XREF)=136264.789 | ------------------------------------------------------------------------------- NBONDS: found 30714 intra-atom interactions NBONDS: found 2909 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.309 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 225.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139634.695 E(kin)=133.912 temperature=225.000 | | Etotal =139500.783 grad(E)=37.629 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=740.319 E(IMPR)=111.092 E(VDW )=1556.955 E(PVDW)=58.401 | | E(HARM)=0.000 E(XREF)=136290.455 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.309 NBONDS: found 30711 intra-atom interactions NBONDS: found 2911 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.351 XTAREXPR: ->[WORKING SET] monitor= 0.310 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139638.024 E(kin)=133.912 temperature=225.000 | | Etotal =139504.113 grad(E)=37.421 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=735.701 E(IMPR)=111.092 E(VDW )=1523.448 E(PVDW)=57.894 | | E(HARM)=0.000 E(XREF)=136332.417 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.351 XTAREXPR: ->[WORKING SET] monitor= 0.310 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 200.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139642.195 E(kin)=119.033 temperature=200.000 | | Etotal =139523.162 grad(E)=37.469 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=734.148 E(IMPR)=111.092 E(VDW )=1524.482 E(PVDW)=57.960 | | E(HARM)=0.000 E(XREF)=136351.919 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.310 NBONDS: found 30720 intra-atom interactions NBONDS: found 2919 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.309 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139620.792 E(kin)=119.033 temperature=200.000 | | Etotal =139501.760 grad(E)=37.287 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=735.862 E(IMPR)=111.092 E(VDW )=1524.079 E(PVDW)=56.573 | | E(HARM)=0.000 E(XREF)=136330.593 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 175.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139598.534 E(kin)=104.154 temperature=175.000 | | Etotal =139494.381 grad(E)=37.302 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=738.323 E(IMPR)=111.092 E(VDW )=1527.737 E(PVDW)=56.064 | | E(HARM)=0.000 E(XREF)=136317.604 | ------------------------------------------------------------------------------- NBONDS: found 30737 intra-atom interactions NBONDS: found 2924 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.309 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.309 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139600.685 E(kin)=104.154 temperature=175.000 | | Etotal =139496.531 grad(E)=37.466 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=743.899 E(IMPR)=111.092 E(VDW )=1538.571 E(PVDW)=56.683 | | E(HARM)=0.000 E(XREF)=136302.725 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.309 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 150.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139580.838 E(kin)=89.275 temperature=150.000 | | Etotal =139491.563 grad(E)=37.470 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=742.970 E(IMPR)=111.092 E(VDW )=1537.640 E(PVDW)=57.360 | | E(HARM)=0.000 E(XREF)=136298.941 | ------------------------------------------------------------------------------- NBONDS: found 30731 intra-atom interactions NBONDS: found 2911 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.352 XTAREXPR: ->[WORKING SET] monitor= 0.309 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139487.066 E(kin)=89.275 temperature=150.000 | | Etotal =139397.792 grad(E)=37.362 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=735.967 E(IMPR)=111.092 E(VDW )=1530.718 E(PVDW)=57.049 | | E(HARM)=0.000 E(XREF)=136219.404 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.351 XTAREXPR: ->[WORKING SET] monitor= 0.309 NBONDS: found 30729 intra-atom interactions NBONDS: found 2908 symmetry-atom interactions CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 125.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139509.286 E(kin)=74.395 temperature=125.000 | | Etotal =139434.890 grad(E)=37.308 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=735.338 E(IMPR)=111.092 E(VDW )=1525.070 E(PVDW)=56.370 | | E(HARM)=0.000 E(XREF)=136263.459 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.351 XTAREXPR: ->[WORKING SET] monitor= 0.309 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139507.134 E(kin)=74.395 temperature=125.000 | | Etotal =139432.738 grad(E)=37.260 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=734.048 E(IMPR)=111.092 E(VDW )=1513.986 E(PVDW)=53.893 | | E(HARM)=0.000 E(XREF)=136276.159 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.351 XTAREXPR: ->[WORKING SET] monitor= 0.309 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 100.000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139517.577 E(kin)=59.516 temperature=100.000 | | Etotal =139458.061 grad(E)=37.227 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=734.301 E(IMPR)=111.092 E(VDW )=1511.389 E(PVDW)=53.659 | | E(HARM)=0.000 E(XREF)=136304.058 | ------------------------------------------------------------------------------- NBONDS: found 30745 intra-atom interactions NBONDS: found 2915 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.309 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139472.856 E(kin)=59.516 temperature=100.000 | | Etotal =139413.340 grad(E)=37.183 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=739.560 E(IMPR)=111.092 E(VDW )=1517.291 E(PVDW)=55.440 | | E(HARM)=0.000 E(XREF)=136246.397 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.309 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 75.0000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139481.966 E(kin)=44.637 temperature=75.000 | | Etotal =139437.329 grad(E)=37.208 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=740.290 E(IMPR)=111.092 E(VDW )=1520.293 E(PVDW)=56.136 | | E(HARM)=0.000 E(XREF)=136265.958 | ------------------------------------------------------------------------------- NBONDS: found 30745 intra-atom interactions NBONDS: found 2912 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.308 ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139446.620 E(kin)=44.637 temperature=75.000 | | Etotal =139401.983 grad(E)=37.289 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=736.653 E(IMPR)=111.092 E(VDW )=1526.999 E(PVDW)=56.903 | | E(HARM)=0.000 E(XREF)=136226.776 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 50.0000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139412.798 E(kin)=29.758 temperature=50.000 | | Etotal =139383.040 grad(E)=37.293 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=735.306 E(IMPR)=111.092 E(VDW )=1528.125 E(PVDW)=56.771 | | E(HARM)=0.000 E(XREF)=136208.185 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.308 NBONDS: found 30734 intra-atom interactions NBONDS: found 2915 symmetry-atom interactions ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139405.406 E(kin)=29.758 temperature=50.000 | | Etotal =139375.648 grad(E)=37.275 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=731.902 E(IMPR)=111.092 E(VDW )=1525.976 E(PVDW)=56.709 | | E(HARM)=0.000 E(XREF)=136206.407 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.308 CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 25.0000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as true CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> timestep=$time_step Torsion Dynamics> nstep=$md_steps Torsion Dynamics> nprint=5 Torsion Dynamics> cmremove=false Torsion Dynamics> vscaling=true TORMD: velocity rescaling (VSCAle) enabled Torsion Dynamics> temperature=$curr_temp Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- TORMD3: number of degrees of freedom= 599 -------------------------- Initial Conditions --------------------------------- | E(kin)+E(total)=139417.062 E(kin)=14.879 temperature=25.000 | | Etotal =139402.183 grad(E)=37.252 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=731.813 E(IMPR)=111.092 E(VDW )=1523.508 E(PVDW)=56.702 | | E(HARM)=0.000 E(XREF)=136235.508 | ------------------------------------------------------------------------------- ------------------ step= 5 at 0.02000 ps ----------------------------- | E(kin)+E(total)=139372.179 E(kin)=14.879 temperature=25.000 | | Etotal =139357.300 grad(E)=37.170 E(BOND)=192.668 E(ANGL)=550.892 | | E(DIHE)=733.690 E(IMPR)=111.092 E(VDW )=1513.715 E(PVDW)=55.900 | | E(HARM)=0.000 E(XREF)=136199.343 | ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then NEXTCD: condition evaluated as false CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) EVALUATE: symbol $CURR_TEMP set to 0.00000 (real) CNSsolve> end loop cool CNSsolve> while ( $curr_temp > 0.0 ) loop cool NEXTCD: condition evaluated as false CNSsolve> if ( &md_type = "torsion" ) then CNSsolve> dynamics torsion CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=5 CNSsolve> cmremove=false CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) CNSsolve> end loop cool CNSsolve> CNSsolve> do (mass=store6) ( all ) SELRPN: 1275 atoms have been selected out of 1275 CNSsolve> CNSsolve> if ( &md_type = "torsion" ) then NEXTCD: condition evaluated as true CNSsolve> dynamics torsion Torsion Dynamics> nstep = 0 Torsion Dynamics> cmremove=false Torsion Dynamics> topology +++++++++++++++++++++++++++++ Torsion Topology +++++++++++++++++++++++++++++++ WARNING: The previous topology will be inherited. Issue a RESET statement to modify it. Topology statements will not be parsed. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Torsion Topology> reset Torsion Topology> end Torsion Dynamics> end -------------------------- Torsion Angle Dynamics ----------------------------- WARNING: Velocities taken from last torsion angle dynamics step. ------------------------------------------------------------------------------- CNSsolve> end if CNSsolve> CNSsolve> parameter PARRDR> nbonds NBDSET> repel=$repel_old rcon=$rcon_old NBDSET> end PARRDR> end CNSsolve> end if CNSsolve> CNSsolve> xray XRAY> tolerance=0.0 lookup=false XRAY> end CNSsolve> CNSsolve> if ( &wa < 0 ) then NEXTCD: condition evaluated as true CNSsolve> @@CNS_XTALMODULE:getweight ( ASSFIL: file /sw/share/xtal/cns_solve_1.1/modules/xtal/getweight opened. CNSsolve>! Module file: getweight CNSsolve>! CNSsolve>! CNS module CNSsolve>! ********** CNSsolve>! CNSsolve>! Authors: Axel T. Brunger and Paul Adams CNSsolve>! CNSsolve>! copyright Yale University CNSsolve>! CNSsolve>! Function: CNSsolve>! Calculate the weight for the crystallographic energy term CNSsolve>! CNSsolve>! Requirements: CNSsolve>! To be called from the main level CNSsolve>! Uses comparision coordinate set and also vx, vy, vz CNSsolve>! This module uses store5 CNSsolve> CNSsolve>module {getweight} MODULE-DECLARATION>( MODULE-DECLARATION> &selected=(all); MODULE-DECLARATION> &fixed=(none); MODULE-DECLARATION> &wa=$wa_temp; MODULE-DECLARATION>) MODULE-INVOCATION> selected=&atom_select; &_2_SELECTED set to &_1_ATOM_SELECT MODULE-INVOCATION> fixed=(store7); &_2_FIXED set to ( store7 ) MODULE-INVOCATION> ) CNSsolve> CNSsolve>set message ? end MESSage=NORM CNSsolve>evaluate ($message_old=$result) EVALUATE: symbol $MESSAGE_OLD set to "NORM" (string) CNSsolve>set echo ? end ECHO=TRUE {ON} CNSsolve>evaluate ($echo_old=$result) EVALUATE: symbol $ECHO_OLD set to TRUE (logical) CNSsolve>if ( $log_level = verbose ) then NEXTCD: condition evaluated as false CNSsolve> set echo=on message=normal end CNSsolve>else CNSsolve> set echo=off message=off end Program version= 1.1 File version= 1.1 SEED= 0.14783E+10 POWELL: number of degrees of freedom= 3657 NBONDS: generating intra-molecular exclusion list with mode= 5 MAKINB: mode 5 found 2914 exclusions and 1876 interactions(1-4) NBONDS: found 30735 intra-atom interactions NBONDS: found 2911 symmetry-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =1007.661 grad(E)=9.987 E(BOND)=24.552 E(ANGL)=154.714 | | E(DIHE)=564.550 E(IMPR)=39.377 E(VDW )=214.710 E(PVDW)=9.759 | | E(HARM)=0.000 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum DCART: velocity rescaling (VSCAling) enabled CENMAS: Information about center of free masses position [A] : -15.86510 13.44362 -1.65987 velocity [A/ps] : -0.05558 -0.07721 -0.10985 ang. mom. [amu A/ps] : -44435.22058 -15964.11317 11963.94725 kin. ener. [Kcal/mol] : 0.43103 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -15.86510 13.44362 -1.65987 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 -------------------------- Cartesian dynamics start --------------------------- | E(kin)+E(total)=2097.735 E(kin)=1090.074 temperature=300.000 | | Etotal =1007.661 grad(E)=9.987 E(BOND)=24.552 E(ANGL)=154.714 | | E(DIHE)=564.550 E(IMPR)=39.377 E(VDW )=214.710 E(PVDW)=9.759 | | E(HARM)=0.000 | ------------------------------------------------------------------------------- NBONDS: found 30681 intra-atom interactions NBONDS: found 2880 symmetry-atom interactions NBONDS: found 30685 intra-atom interactions NBONDS: found 2860 symmetry-atom interactions NBONDS: found 30654 intra-atom interactions NBONDS: found 2843 symmetry-atom interactions -------------------- final step= 200 at 0.10000 ps --------------------- | E(kin)+E(total)=2508.888 E(kin)=1090.074 temperature=300.000 | | Etotal =1418.814 grad(E)=38.901 E(BOND)=244.889 E(ANGL)=358.695 | | E(DIHE)=412.078 E(IMPR)=116.270 E(VDW )=276.207 E(PVDW)=10.676 | | E(HARM)=0.000 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : -15.86724 13.43896 -1.65954 velocity [A/ps] : -0.04031 -0.09641 0.01003 ang. mom. [amu A/ps] : -4921.03310 49499.16568 -13423.76470 kin. ener. [Kcal/mol] : 0.22495 --------------- cycle= 3 -------------------------------------------------- | Etotal =1418.814 grad(E)=38.901 E(BOND)=244.889 E(ANGL)=358.695 | | E(DIHE)=412.078 E(IMPR)=116.270 E(VDW )=276.207 E(PVDW)=10.676 | | E(HARM)=0.000 | ------------------------------------------------------------------------------- SHOW: sum over selected elements = 1219.000000 SHOW: sum over selected elements = 5786290.229424 --------------- cycle= 4 -------------------------------------------------- | Etotal =39003.411 grad(E)=39.310 E(BOND)=244.889 E(ANGL)=358.695 | | E(DIHE)=412.078 E(IMPR)=116.270 E(VDW )=276.207 E(PVDW)=10.676 | | E(HARM)=0.000 E(XREF)=37584.596 | ------------------------------------------------------------------------------- SHOW: rms deviation from aver of selected elements = 155.753267 SHOW: rms deviation from aver of selected elements = 76.561209 SHOW: sum over selected elements = 100999.953746 getweight: optimal weight= 3.78451 CNSsolve> end if CNSsolve> CNSsolve> if ( &mini_steps > 0 ) then NEXTCD: condition evaluated as true CNSsolve> minimize lbfgs LBFGS> nstep=&mini_steps LBFGS> drop=10.0 nprint=10 LBFGS> end LBFGS: number of degrees of freedom= 3657 NBONDS: found 30735 intra-atom interactions NBONDS: found 2911 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.308 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.348 XTAREXPR: ->[WORKING SET] monitor= 0.304 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.307 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.350 XTAREXPR: ->[WORKING SET] monitor= 0.307 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.349 XTAREXPR: ->[WORKING SET] monitor= 0.305 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.348 XTAREXPR: ->[WORKING SET] monitor= 0.304 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.347 XTAREXPR: ->[WORKING SET] monitor= 0.302 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.346 XTAREXPR: ->[WORKING SET] monitor= 0.301 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.346 XTAREXPR: ->[WORKING SET] monitor= 0.300 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.345 XTAREXPR: ->[WORKING SET] monitor= 0.299 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.344 XTAREXPR: ->[WORKING SET] monitor= 0.297 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.344 XTAREXPR: ->[WORKING SET] monitor= 0.297 ------------------------------ cycle= 10 ----------------------------------- | Etotal =138461.625 grad(E)=15.406 E(BOND)=142.719 E(ANGL)=343.017 | | E(DIHE)=684.594 E(IMPR)=70.431 E(VDW )=231.675 E(PVDW)=16.746 | | E(HARM)=0.000 E(XREF)=136972.442 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.343 XTAREXPR: ->[WORKING SET] monitor= 0.296 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.342 XTAREXPR: ->[WORKING SET] monitor= 0.294 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.341 XTAREXPR: ->[WORKING SET] monitor= 0.293 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.340 XTAREXPR: ->[WORKING SET] monitor= 0.292 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.340 XTAREXPR: ->[WORKING SET] monitor= 0.291 NBONDS: found 30733 intra-atom interactions NBONDS: found 2888 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.338 XTAREXPR: ->[WORKING SET] monitor= 0.290 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.337 XTAREXPR: ->[WORKING SET] monitor= 0.289 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.336 XTAREXPR: ->[WORKING SET] monitor= 0.288 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.335 XTAREXPR: ->[WORKING SET] monitor= 0.288 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.333 XTAREXPR: ->[WORKING SET] monitor= 0.286 ------------------------------ cycle= 20 ----------------------------------- | Etotal =137792.051 grad(E)=19.797 E(BOND)=146.437 E(ANGL)=373.389 | | E(DIHE)=677.339 E(IMPR)=86.459 E(VDW )=260.245 E(PVDW)=25.235 | | E(HARM)=0.000 E(XREF)=136222.946 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.332 XTAREXPR: ->[WORKING SET] monitor= 0.286 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.332 XTAREXPR: ->[WORKING SET] monitor= 0.285 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.331 XTAREXPR: ->[WORKING SET] monitor= 0.285 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.329 XTAREXPR: ->[WORKING SET] monitor= 0.284 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.329 XTAREXPR: ->[WORKING SET] monitor= 0.283 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.328 XTAREXPR: ->[WORKING SET] monitor= 0.283 NBONDS: found 30754 intra-atom interactions NBONDS: found 2895 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.328 XTAREXPR: ->[WORKING SET] monitor= 0.282 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.327 XTAREXPR: ->[WORKING SET] monitor= 0.282 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.326 XTAREXPR: ->[WORKING SET] monitor= 0.281 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.326 XTAREXPR: ->[WORKING SET] monitor= 0.281 ------------------------------ cycle= 30 ----------------------------------- | Etotal =137394.041 grad(E)=13.143 E(BOND)=109.720 E(ANGL)=373.277 | | E(DIHE)=689.278 E(IMPR)=79.378 E(VDW )=290.812 E(PVDW)=30.118 | | E(HARM)=0.000 E(XREF)=135821.458 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.325 XTAREXPR: ->[WORKING SET] monitor= 0.281 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.325 XTAREXPR: ->[WORKING SET] monitor= 0.280 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.324 XTAREXPR: ->[WORKING SET] monitor= 0.280 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.323 XTAREXPR: ->[WORKING SET] monitor= 0.280 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.323 XTAREXPR: ->[WORKING SET] monitor= 0.279 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.322 XTAREXPR: ->[WORKING SET] monitor= 0.279 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.321 XTAREXPR: ->[WORKING SET] monitor= 0.279 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.321 XTAREXPR: ->[WORKING SET] monitor= 0.279 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.320 XTAREXPR: ->[WORKING SET] monitor= 0.279 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.320 XTAREXPR: ->[WORKING SET] monitor= 0.278 ------------------------------ cycle= 40 ----------------------------------- | Etotal =137148.734 grad(E)=8.124 E(BOND)=89.985 E(ANGL)=347.910 | | E(DIHE)=684.509 E(IMPR)=60.293 E(VDW )=287.490 E(PVDW)=31.382 | | E(HARM)=0.000 E(XREF)=135647.165 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.319 XTAREXPR: ->[WORKING SET] monitor= 0.278 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.319 XTAREXPR: ->[WORKING SET] monitor= 0.278 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.319 XTAREXPR: ->[WORKING SET] monitor= 0.278 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.318 XTAREXPR: ->[WORKING SET] monitor= 0.278 NBONDS: found 30792 intra-atom interactions NBONDS: found 2894 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.318 XTAREXPR: ->[WORKING SET] monitor= 0.277 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.318 XTAREXPR: ->[WORKING SET] monitor= 0.277 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.318 XTAREXPR: ->[WORKING SET] monitor= 0.277 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.317 XTAREXPR: ->[WORKING SET] monitor= 0.277 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.317 XTAREXPR: ->[WORKING SET] monitor= 0.277 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.317 XTAREXPR: ->[WORKING SET] monitor= 0.277 ------------------------------ cycle= 50 ----------------------------------- | Etotal =137005.092 grad(E)=6.833 E(BOND)=74.899 E(ANGL)=345.206 | | E(DIHE)=683.689 E(IMPR)=58.980 E(VDW )=288.115 E(PVDW)=27.358 | | E(HARM)=0.000 E(XREF)=135526.845 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.317 XTAREXPR: ->[WORKING SET] monitor= 0.276 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.317 XTAREXPR: ->[WORKING SET] monitor= 0.276 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.317 XTAREXPR: ->[WORKING SET] monitor= 0.276 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.317 XTAREXPR: ->[WORKING SET] monitor= 0.276 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.317 XTAREXPR: ->[WORKING SET] monitor= 0.276 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.317 XTAREXPR: ->[WORKING SET] monitor= 0.276 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.275 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.275 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.275 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.275 ------------------------------ cycle= 60 ----------------------------------- | Etotal =136895.192 grad(E)=6.063 E(BOND)=78.044 E(ANGL)=352.692 | | E(DIHE)=677.242 E(IMPR)=64.873 E(VDW )=290.043 E(PVDW)=25.908 | | E(HARM)=0.000 E(XREF)=135406.390 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.275 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.275 NBONDS: found 30791 intra-atom interactions NBONDS: found 2890 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.274 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.274 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.274 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.274 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.274 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.274 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.274 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.274 ------------------------------ cycle= 70 ----------------------------------- | Etotal =136806.729 grad(E)=6.067 E(BOND)=77.190 E(ANGL)=360.296 | | E(DIHE)=670.437 E(IMPR)=64.153 E(VDW )=291.403 E(PVDW)=25.643 | | E(HARM)=0.000 E(XREF)=135317.607 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.273 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.273 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.273 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.273 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.273 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.273 NBONDS: found 30808 intra-atom interactions NBONDS: found 2881 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.273 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.273 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.273 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.273 ------------------------------ cycle= 80 ----------------------------------- | Etotal =136745.722 grad(E)=4.084 E(BOND)=77.171 E(ANGL)=353.525 | | E(DIHE)=670.769 E(IMPR)=62.463 E(VDW )=292.581 E(PVDW)=25.381 | | E(HARM)=0.000 E(XREF)=135263.831 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.273 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.273 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 ------------------------------ cycle= 90 ----------------------------------- | Etotal =136707.692 grad(E)=3.340 E(BOND)=74.305 E(ANGL)=351.491 | | E(DIHE)=668.376 E(IMPR)=61.150 E(VDW )=293.663 E(PVDW)=25.032 | | E(HARM)=0.000 E(XREF)=135233.675 | ------------------------------------------------------------------------------- FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 NBONDS: found 30852 intra-atom interactions NBONDS: found 2863 symmetry-atom interactions FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XTAREXPR: ->[TEST SET] monitor= 0.316 XTAREXPR: ->[WORKING SET] monitor= 0.272 ------------------------------ cycle= 100 ----------------------------------- | Etotal =136683.386 grad(E)=3.331 E(BOND)=71.742 E(ANGL)=349.362 | | E(DIHE)=668.502 E(IMPR)=59.378 E(VDW )=292.986 E(PVDW)=25.276 | | E(HARM)=0.000 E(XREF)=135216.141 | ------------------------------------------------------------------------------- LBFGS: normal termination - NSTEP limit reached CNSsolve> end if CNSsolve> CNSsolve> evaluate ($cycle=$cycle+1) EVALUATE: symbol $CYCLE set to 2.00000 (real) CNSsolve> CNSsolve> xray XRAY> XRAY> tselection=(map_active=1) XRAY> XRAY> if ( &map_type = "gradient" ) then NEXTCD: condition evaluated as false XRAY> predict XRAY> mode=dtarget(fcalc) XRAY> to=dtarg XRAY> selection=( map_active=1 ) XRAY> atomselection=( &atom_select and not store8 ) XRAY> end XRAY> do (dave=dave+dtarg) (all) XRAY> else XRAY> predict PREDict> mode=reciprocal PREDict> to=fcalc PREDict> selection=( all_active=1 ) Total of 10271 structure factor elements were selected. PREDict> atomselection=( &atom_select and not store8 ) SELRPN: 1275 atoms have been selected out of 1275 PREDict> end FCALC: #scatt.= 1275 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 96, 96, 144] and sublattice [ 96( 97), 96( 97), 144] XRAY> end if XRAY> do (fcave=fcave+fcalc) (all) Total of 10271 structure factor elements were selected. XRAY> do (fpave=fpave+fbulk) (all) Total of 10271 structure factor elements were selected. XRAY> do (foave=foave+&STRIP%obs_f) (all) Total of 10271 structure factor elements were selected. XRAY> end CNSsolve> CNSsolve> end loop main CNSsolve> while ( $cycle <= $ave_cycle ) loop main NEXTCD: condition evaluated as false CNSsolve> CNSsolve> coord init end CNSsolve> coord @@&coordinate_infile_$cycle CNSsolve> CNSsolve> xray CNSsolve> do (&STRIP%obs_f=fobs_orig) (all) CNSsolve> do (&STRIP%obs_sigf=sigma_orig) (all) CNSsolve> if ( &BLANK%obs_i = false ) then CNSsolve> do (&STRIP%obs_i=iobs_orig) (all) CNSsolve> do (&STRIP%obs_sigi=sigi_orig) (all) CNSsolve> end if CNSsolve> end CNSsolve> CNSsolve> xray CNSsolve> predict CNSsolve> mode=reciprocal CNSsolve> to=fcalc CNSsolve> selection=( all_active=1 ) CNSsolve> atomselection=( &atom_select and not store8 ) CNSsolve> end CNSsolve> end CNSsolve> CNSsolve> @@CNS_XTALMODULE:scalenbulk (bscale=&bscale; CNSsolve> sel=( ref_active=1 ); CNSsolve> sel_test=( tst_active=1 ); CNSsolve> res_bscale=&low_res_bscale; CNSsolve> atom_select=( &atom_select ); CNSsolve> bulk_sol=&bulk_sol; CNSsolve> bulk_mask=&bulk_mask_infile; CNSsolve> bulk_atoms=( &atom_select ); CNSsolve> sol_k=&sol_k; CNSsolve> sol_b=&sol_b; CNSsolve> fcalc=fcalc; CNSsolve> fobs=&STRIP%obs_f; CNSsolve> sigma=&STRIP%obs_sigf; CNSsolve> iobs=$STRIP%obs_i; CNSsolve> sigi=$STRIP%obs_sigi; CNSsolve> fpart=fbulk; CNSsolve> B2_11=$aniso_11; CNSsolve> B2_22=$aniso_22; CNSsolve> B2_33=$aniso_33; CNSsolve> B2_12=$aniso_12; CNSsolve> B2_13=$aniso_13; CNSsolve> B2_23=$aniso_23; CNSsolve> trace=$trace; CNSsolve> sol_k_ref=$sol_k_ref; CNSsolve> sol_b_ref=$sol_b_ref; CNSsolve> b_too_low=$low_b_flag;) CNSsolve> CNSsolve> xray CNSsolve> CNSsolve> tselection=(ref_active=1) CNSsolve> CNSsolve> @@CNS_XTALMODULE:refinementtarget (target=&reftarget; CNSsolve> sig_sigacv=0.07; CNSsolve> mbins=&target_bins; CNSsolve> fobs=&STRIP%obs_f; CNSsolve> sigma=&STRIP%obs_sigf; CNSsolve> weight=$STRIP%obs_w; CNSsolve> iobs=$STRIP%obs_i; CNSsolve> sigi=$STRIP%obs_sigi; CNSsolve> test=tst_active; CNSsolve> fcalc=fcalc; CNSsolve> fpart=fbulk; CNSsolve> pa=&STRIP%obs_pa; CNSsolve> pb=&STRIP%obs_pb; CNSsolve> pc=&STRIP%obs_pc; CNSsolve> pd=&STRIP%obs_pd; CNSsolve> phase=&STRIP%obs_phase; CNSsolve> fom=&STRIP%obs_fom; CNSsolve> sel=(ref_active=1); CNSsolve> sel_test=(tst_active=1); CNSsolve> statistics=true;) CNSsolve> end CNSsolve> CNSsolve> if ( &anneal = true ) then CNSsolve> CNSsolve> xray CNSsolve> tolerance=0.2 lookup=true CNSsolve> end CNSsolve> CNSsolve> do ( harm=0 ) ( all ) CNSsolve> do ( harmonic=&k_harmonic ) ( &atom_harm ) CNSsolve> do ( harmonic=20 ) ( store9 or store8 ) CNSsolve> do ( refx=x ) ( all ) CNSsolve> do ( refy=y ) ( all ) CNSsolve> do ( refz=z ) ( all ) CNSsolve> flags include harm end CNSsolve> CNSsolve> if ( &wa < 0 ) then CNSsolve> @@CNS_XTALMODULE:getweight ( CNSsolve> selected=&atom_select; CNSsolve> fixed=(store7); CNSsolve> ) CNSsolve> end if CNSsolve> CNSsolve> parameter CNSsolve> nbonds CNSsolve> repel ? evaluate ($repel_old=$result) CNSsolve> rcon ? evaluate ($rcon_old=$result) CNSsolve> if ($repel_old =1 ) then CNSsolve> repel=1. rcon=100. CNSsolve> else CNSsolve> repel=.75 rcon=50. CNSsolve> end if CNSsolve> end CNSsolve> end CNSsolve> CNSsolve> do (fbeta=$fbeta) ( ( &atom_select ) and not (store7) ) CNSsolve> CNSsolve> do (vx=maxwell($start_temp)) (&atom_select and not (store7)) CNSsolve> do (vy=maxwell($start_temp)) (&atom_select and not (store7)) CNSsolve> do (vz=maxwell($start_temp)) (&atom_select and not (store7)) CNSsolve> CNSsolve> if ( &md_type = "torsion" ) then CNSsolve> dynamics torsion CNSsolve> topology CNSsolve> CNSsolve> maxlength=&torsion_maxlength CNSsolve> maxchain=&torsion_maxchain CNSsolve> maxtree=&torsion_maxtree CNSsolve> maxbond=&torsion_maxbond CNSsolve> kdihmax = 95. CNSsolve> CNSsolve> CNSsolve>! CNS toppar file: torsionmdmods CNSsolve>! CNSsolve>! Authors: Axel Brunger and Luke Rice CNSsolve>! CNSsolve>! copyright Yale University CNSsolve>! CNSsolve>! Function: CNSsolve>! Applies various patches to torsion angle dynamics CNSsolve>! necessary for certain topologies CNSsolve>! CNSsolve>! Requirements: CNSsolve>! Needs to be called from torsion topology CNSsolve> CNSsolve> CNSsolve>set message ? end CNSsolve>evaluate ($message_old_tmod=$result) CNSsolve>set echo ? end CNSsolve>evaluate ($echo_old_tmod=$result) CNSsolve>if ( $log_level = verbose ) then CNSsolve> set echo=on message=normal end CNSsolve>else CNSsolve> set echo=off message=off end CNSsolve>end if CNSsolve> CNSsolve>checkversion 1.1 CNSsolve> CNSsolve> CNSsolve> {- remove disulfide bond links -} CNSsolve> for $ss_rm_id_1 in id ( name SG ) loop SSRM CNSsolve> for $ss_rm_id_2 in id ( name SG and FOR-clause= bondedto ( id $ss_rm_id_1 ) ) loop SSR2 CNSsolve> if ($ss_rm_id_1 > $ss_rm_id_2) then CNSsolve> free bond ( id $ss_rm_id_1 ) ( id $ss_rm_id_2 ) CNSsolve> end if CNSsolve> end loop SSR2 CNSsolve> end loop SSRM CNSsolve> CNSsolve> {- keep prolines as rigid bodies -} CNSsolve> fix group ( resn PRO and not (name c or name o) ) CNSsolve> CNSsolve> {- free a bond in sugar rings to have control over which bond is broken CNSsolve> by torsion topology -} CNSsolve> for $nucl in id ( tag and ( resn THY or resn CYT or resn GUA or FOR-clause= resn ADE or resn URI )) loop nucl CNSsolve> free bond ( byres (id $nucl) and name C3' ) CNSsolve> ( byres (id $nucl) and name C4' ) CNSsolve> end loop nucl CNSsolve> CNSsolve> {- free a bond in carbohydrates to have control over which bond is broken CNSsolve> by torsion topology -} CNSsolve> for $nucl in id ( tag and ( resn NAG or resn GAL or resn GLC or FOR-clause= resn FUC or resn SIA or resn XYL or FOR-clause= resn MAN )) loop nucl CNSsolve> free bond ( byres (id $nucl) and name C3 ) CNSsolve> ( byres (id $nucl) and name C4 ) CNSsolve> end loop nucl CNSsolve> CNSsolve> {- keep nucleic acid bases rigid -} CNSsolve> fix group ( resn THY and not(name c#' or name h#' or name o#p or CNSsolve> name o#' or name p or name h#t or name o#t)) CNSsolve> fix group ( resn CYT and not(name c#' or name h#' or name o#p or CNSsolve> name o#' or name p or name h#t or name o#t)) CNSsolve> fix group ( resn GUA and not(name c#' or name h#' or name o#p or CNSsolve> name o#' or name p or name h#t or name o#t)) CNSsolve> fix group ( resn ADE and not(name c#' or name h#' or name o#p or CNSsolve> name o#' or name p or name h#t or name o#t)) CNSsolve> fix group ( resn URI and not(name c#' or name h#' or name o#p or CNSsolve> name o#' or name p or name h#t or name o#t)) CNSsolve> CNSsolve> CNSsolve>set message=$message_old_tmod echo=$echo_old_tmod end CNSsolve> CNSsolve> CNSsolve> CNSsolve> fix group ( &atom_rigid ) CNSsolve> CNSsolve> end CNSsolve> nstep=0 CNSsolve> cmremove=true CNSsolve> end CNSsolve> end if CNSsolve> CNSsolve> do (store6=mass) ( all ) CNSsolve> do (mass=max(10,min(30,mass))) ( all ) CNSsolve> CNSsolve> evaluate ( $curr_temp = &temperature ) CNSsolve> while ( $curr_temp > 0.0 ) loop cool CNSsolve> if ( &md_type = "torsion" ) then CNSsolve> dynamics torsion CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=5 CNSsolve> cmremove=false CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> if ( &md_type = "cartesian" ) then CNSsolve> dynamics cartesian CNSsolve> if ($curr_temp=&temperature) then CNSsolve> cmremove=true CNSsolve> else CNSsolve> cmremove=false CNSsolve> end if CNSsolve> timestep=$time_step CNSsolve> nstep=$md_steps CNSsolve> nprint=10 CNSsolve> vscaling=true CNSsolve> temperature=$curr_temp CNSsolve> end CNSsolve> end if CNSsolve> evaluate ( $curr_temp = $curr_temp - &cool_rate ) CNSsolve> end loop cool CNSsolve> CNSsolve> do (mass=store6) ( all ) CNSsolve> CNSsolve> if ( &md_type = "torsion" ) then CNSsolve> dynamics torsion CNSsolve> nstep = 0 CNSsolve> cmremove=false CNSsolve> topology CNSsolve> reset CNSsolve> end CNSsolve> end CNSsolve> end if CNSsolve> CNSsolve> parameter CNSsolve> nbonds CNSsolve> repel=$repel_old rcon=$rcon_old CNSsolve> end CNSsolve> end CNSsolve> end if CNSsolve> CNSsolve> xray CNSsolve> tolerance=0.0 lookup=false CNSsolve> end CNSsolve> CNSsolve> if ( &wa < 0 ) then CNSsolve> @@CNS_XTALMODULE:getweight ( CNSsolve> selected=&atom_select; CNSsolve> fixed=(store7); CNSsolve> ) CNSsolve> end if CNSsolve> CNSsolve> if ( &mini_steps > 0 ) then CNSsolve> minimize lbfgs CNSsolve> nstep=&mini_steps CNSsolve> drop=10.0 nprint=10 CNSsolve> end CNSsolve> end if CNSsolve> CNSsolve> evaluate ($cycle=$cycle+1) CNSsolve> CNSsolve> xray CNSsolve> CNSsolve> tselection=(map_active=1) CNSsolve> CNSsolve> if ( &map_type = "gradient" ) then CNSsolve> predict CNSsolve> mode=dtarget(fcalc) CNSsolve> to=dtarg CNSsolve> selection=( map_active=1 ) CNSsolve> atomselection=( &atom_select and not store8 ) CNSsolve> end CNSsolve> do (dave=dave+dtarg) (all) CNSsolve> else CNSsolve> predict CNSsolve> mode=reciprocal CNSsolve> to=fcalc CNSsolve> selection=( all_active=1 ) CNSsolve> atomselection=( &atom_select and not store8 ) CNSsolve> end CNSsolve> end if CNSsolve> do (fcave=fcave+fcalc) (all) CNSsolve> do (fpave=fpave+fbulk) (all) CNSsolve> do (foave=foave+&STRIP%obs_f) (all) CNSsolve> end CNSsolve> CNSsolve> end loop main CNSsolve> CNSsolve> xray XRAY> if ( &map_type = "gradient" ) then NEXTCD: condition evaluated as false XRAY> do (dave=dave/$ave_cycle) (all) XRAY> end if XRAY> do (fcalc=fcave/$ave_cycle) (all) Total of 10271 structure factor elements were selected. XRAY> do (fbulk=fpave/$ave_cycle) (all) Total of 10271 structure factor elements were selected. XRAY> do (&STRIP%obs_f=foave/$ave_cycle) (all) Total of 10271 structure factor elements were selected. XRAY> @@CNS_XTALMODULE:calculate_r (fobs=&STRIP%obs_f; ASSFIL: file /sw/share/xtal/cns_solve_1.1/modules/xtal/calculate_r opened. XRAY>! Module file: calculate_r XRAY>! XRAY>! CNS module XRAY>! ************ XRAY>! XRAY>! Authors: Axel Brunger and Paul Adams XRAY>! XRAY>! copyright Yale University XRAY>! XRAY>! Function: XRAY>! Calculates crystallographic R-values XRAY>! XRAY>! Requirements: XRAY>! Needs to be called within xray XRAY> XRAY>module {calculate_r} MODULE-DECLARATION> MODULE-DECLARATION>( MODULE-DECLARATION>&fobs=fobs; MODULE-DECLARATION>&fcalc=fcalc; MODULE-DECLARATION>&fpart=fpart; MODULE-DECLARATION>&sel=all; MODULE-DECLARATION>&sel_test=none; MODULE-DECLARATION>&print=false; MODULE-DECLARATION>&output=OUTPUT; MODULE-DECLARATION>&r=$r; MODULE-DECLARATION>&test_r=$test_r; MODULE-DECLARATION>) &_2_FOBS set to &STRIP%_1_OBS_F MODULE-INVOCATION> fcalc=fcalc; &_2_FCALC set to fcalc MODULE-INVOCATION> fpart=fbulk; &_2_FPART set to fbulk MODULE-INVOCATION> sel=(map_active=1); &_2_SEL set to ( map_active = 1 ) MODULE-INVOCATION> sel_test=(tst_active=1); &_2_SEL_TEST set to ( tst_active = 1 ) MODULE-INVOCATION> print=true; &_2_PRINT set to true MODULE-INVOCATION> output=OUTPUT; &_2_OUTPUT set to OUTPUT MODULE-INVOCATION> r=$map_r; &_2_R set to $_1_MAP_R MODULE-INVOCATION> test_r=$map_free_r;) &_2_TEST_R set to $_1_MAP_FREE_R XRAY> XRAY>set message ? end MESSage=NORM XRAY>evaluate ($message_old=$result) EVALUATE: symbol $MESSAGE_OLD set to "NORM" (string) XRAY>set echo ? end ECHO=TRUE {ON} XRAY>evaluate ($echo_old=$result) EVALUATE: symbol $ECHO_OLD set to TRUE (logical) XRAY>if ( $log_level = verbose ) then NEXTCD: condition evaluated as false XRAY> set echo=on message=normal end XRAY>else XRAY> set echo=off message=off end DISPlay-file=OUTPUT Program version= 1.1 File version= 1.1 Sum of 9535 elements = 9535.0000 Sum of 959 elements = 959.0000 ============================================ R-value by resolution for test set ============================================ #bin | resolution range | #refl | 1 6.14 500.01 54 0.3741 2 4.87 6.14 57 0.3899 3 4.26 4.87 46 0.2638 4 3.87 4.26 52 0.3787 5 3.59 3.87 52 0.2362 6 3.38 3.59 73 0.3027 7 3.21 3.38 52 0.2707 8 3.07 3.21 49 0.3460 9 2.95 3.07 48 0.3091 10 2.85 2.95 50 0.2663 11 2.76 2.85 59 0.2962 12 2.68 2.76 56 0.2984 13 2.61 2.68 55 0.2760 14 2.55 2.61 61 0.2812 15 2.49 2.55 41 0.2967 16 2.44 2.49 41 0.3481 17 2.39 2.44 48 0.3320 18 2.34 2.39 46 0.3608 19 2.30 2.34 19 0.2688 #bin | resolution range | #refl | 1 2.30 500.01 959 0.3155 >>>> Overall R-value for test set: 0.315508 ============================================ R-value by resolution for working set ============================================ #bin | resolution range | #refl | 1 6.14 500.01 500 0.3293 2 4.87 6.14 501 0.2841 3 4.26 4.87 488 0.2406 4 3.87 4.26 488 0.2595 5 3.59 3.87 497 0.2577 6 3.38 3.59 452 0.2479 7 3.21 3.38 491 0.2444 8 3.07 3.21 472 0.2765 9 2.95 3.07 488 0.2637 10 2.85 2.95 467 0.2543 11 2.76 2.85 447 0.2772 12 2.68 2.76 455 0.2859 13 2.61 2.68 452 0.2700 14 2.55 2.61 439 0.2961 15 2.49 2.55 437 0.2696 16 2.44 2.49 435 0.2847 17 2.39 2.44 433 0.2757 18 2.34 2.39 423 0.3121 19 2.30 2.34 211 0.2909 #bin | resolution range | #refl | 1 2.30 500.01 8576 0.2718 >>>> Overall R-value for working set: 0.271785 XRAY> end CNSsolve> CNSsolve> xray XRAY> declare name=map_phase domain=reciprocal type=real end XDECLARE: Object MAP_PHASE has been declared. XRAY> declare name=map_fom domain=reciprocal type=real end XDECLARE: Object MAP_FOM has been declared. XRAY> declare name=map_scale domain=reciprocal type=real end XDECLARE: Object MAP_SCALE has been declared. XRAY> end CNSsolve> CNSsolve> if ( &map_type = "unweighted" ) then NEXTCD: condition evaluated as false CNSsolve> CNSsolve> xray CNSsolve> CNSsolve> do (map_phase=phase(fcalc+fbulk)) (all) CNSsolve> CNSsolve> do (total=fcalc+fbulk) (all) CNSsolve> multiscale CNSsolve> bfmin=-40 bfmax=40 CNSsolve> set1=&STRIP%obs_f k1=-1 b1=0 CNSsolve> set2=total b2=0 CNSsolve> selection=(map_active=1 and d <= &low_res_bscale) CNSsolve> end CNSsolve> do (map_scale=$k2) (all) CNSsolve> CNSsolve> do (map_fom=1.0) (all) CNSsolve> CNSsolve> end CNSsolve> CNSsolve> elseif ( &map_type = "sigmaa" ) then NEXTCD: condition evaluated as true CNSsolve> CNSsolve> xray XRAY> XRAY> do (map_phase=phase(fcalc+fbulk)) (all) XSFAL: allocating space for real reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> XRAY> declare name=m domain=reciprocal type=complex end XDECLARE: Object M has been declared. XRAY> declare name=mod_fom domain=reciprocal type=real end XDECLARE: Object MOD_FOM has been declared. XRAY> declare name=mod_x domain=reciprocal type=real end XDECLARE: Object MOD_X has been declared. XRAY> declare name=mod_pa domain=reciprocal type=real end XDECLARE: Object MOD_PA has been declared. XRAY> declare name=mod_pb domain=reciprocal type=real end XDECLARE: Object MOD_PB has been declared. XRAY> declare name=mod_pc domain=reciprocal type=real end XDECLARE: Object MOD_PC has been declared. XRAY> declare name=mod_pd domain=reciprocal type=real end XDECLARE: Object MOD_PD has been declared. XRAY> declare name=mod_dd domain=reciprocal type=real end XDECLARE: Object MOD_DD has been declared. XRAY> XRAY> @CNS_XTALMODULE:fomsigmaacv ( sig_sigacv=0.07; ASSFIL: file /sw/share/xtal/cns_solve_1.1/modules/xtal/fomsigmaacv opened. XRAY>! Module file: fom_sigmaacv XRAY>! XRAY>! CNS module XRAY>! ********** XRAY>! XRAY>! Authors: Axel Brunger and Paul Adams XRAY>! XRAY>! copyright Yale University XRAY>! XRAY>! Function: XRAY>! Calculates FOM from cross-validated sigmaa estimates XRAY>! XRAY>! Requirements: XRAY>! Needs to be called within xray XRAY> XRAY>module {fomsigmaacv} MODULE-DECLARATION> MODULE-DECLARATION>( MODULE-DECLARATION> &sig_sigacv=0.07; {real} MODULE-DECLARATION> &mbins=10; {real} MODULE-DECLARATION> &statistics=false; {logical} MODULE-DECLARATION> &fobs=fobs; {string} MODULE-DECLARATION> &fcalc=fcalc; {string} MODULE-DECLARATION> &fpart=fpart; {string} MODULE-DECLARATION> &test=test; {string} MODULE-DECLARATION> &sel=(all); {selection} MODULE-DECLARATION> &sel_test=none; {selection} MODULE-DECLARATION> &fom=fom; {string} MODULE-DECLARATION> &x=x; {string} MODULE-DECLARATION> &pa=pa; {string} MODULE-DECLARATION> &pb=pb; {string} MODULE-DECLARATION> &pc=pc; {string} MODULE-DECLARATION> &pd=pd; {string} MODULE-DECLARATION> &dd=dd; {string} MODULE-DECLARATION>) &_2_SIG_SIGACV set to 0.07 MODULE-INVOCATION> mbins=&target_bins; &_2_MBINS set to &_1_TARGET_BINS MODULE-INVOCATION> statistics=true; &_2_STATISTICS set to true MODULE-INVOCATION> fobs=&STRIP%obs_f; &_2_FOBS set to &STRIP%_1_OBS_F MODULE-INVOCATION> fcalc=fcalc; &_2_FCALC set to fcalc MODULE-INVOCATION> fpart=fbulk; &_2_FPART set to fbulk MODULE-INVOCATION> test=tst_active; &_2_TEST set to tst_active MODULE-INVOCATION> sel=(map_active=1); &_2_SEL set to ( map_active = 1 ) MODULE-INVOCATION> sel_test=(tst_active=1); &_2_SEL_TEST set to ( tst_active = 1 ) MODULE-INVOCATION> fom=mod_fom; &_2_FOM set to mod_fom MODULE-INVOCATION> x=mod_x; &_2_X set to mod_x MODULE-INVOCATION> pa=mod_pa; &_2_PA set to mod_pa MODULE-INVOCATION> pb=mod_pb; &_2_PB set to mod_pb MODULE-INVOCATION> pc=mod_pc; &_2_PC set to mod_pc MODULE-INVOCATION> pd=mod_pd; &_2_PD set to mod_pd MODULE-INVOCATION> dd=mod_dd; ) &_2_DD set to mod_dd XRAY> XRAY>set message ? end MESSage=NORM XRAY>evaluate ($message_old=$result) EVALUATE: symbol $MESSAGE_OLD set to "NORM" (string) XRAY>set echo ? end ECHO=TRUE {ON} XRAY>evaluate ($echo_old=$result) EVALUATE: symbol $ECHO_OLD set to TRUE (logical) XRAY>if ( $log_level = verbose ) then NEXTCD: condition evaluated as false XRAY> set echo=on message=normal end XRAY>else XRAY> set echo=off message=off end Program version= 1.1 File version= 1.1 Sum of 959 elements = 959.0000 Sum of 959 elements = 959.0000 Sum of 9535 elements = 9535.0000 Sum of 0 elements = 0.0000 XSIGMAACV: Overall sigma for line restraint is 0.07000000 XSIGMAACV: gradient converged XSIGMAACV: Refinement of SIGMAA has converged Overall mean FOM is 0.79454 #bin | resolution range | #refl | 1 6.14 500.01 554 0.6481 0.7810 0.7701 0.9946 0.9940 2 4.87 6.14 558 0.7237 0.8348 0.7892 1.0000 1.0000 3 4.26 4.87 534 0.8090 0.8918 1.0402 0.9998 0.9996 4 3.87 4.26 540 0.7331 0.8394 0.8764 1.0000 1.0000 5 3.59 3.87 549 0.8213 0.8961 0.8777 0.9999 0.9998 6 3.38 3.59 525 0.8183 0.8914 1.0222 1.0000 1.0000 7 3.21 3.38 543 0.8208 0.8904 0.9688 0.9978 0.9977 8 3.07 3.21 521 0.7443 0.8423 0.9051 1.0000 1.0000 9 2.95 3.07 536 0.7829 0.8701 0.9565 1.0000 1.0000 10 2.85 2.95 517 0.8080 0.8738 0.9014 1.0000 1.0000 11 2.76 2.85 506 0.8121 0.8623 0.8802 1.0000 1.0000 12 2.68 2.76 511 0.8115 0.8671 0.8989 0.9958 0.9971 13 2.61 2.68 507 0.8191 0.8675 0.9031 1.0000 1.0000 14 2.55 2.61 500 0.8388 0.8826 0.9814 1.0000 1.0000 15 2.49 2.55 478 0.8224 0.8539 0.8804 1.0000 1.0000 16 2.44 2.49 476 0.7574 0.8093 0.9403 1.0000 1.0000 17 2.39 2.44 481 0.7262 0.7748 0.7536 0.9997 1.0000 18 2.34 2.39 469 0.7562 0.7905 0.8432 1.0000 1.0000 19 2.30 2.34 230 0.8340 0.8593 0.7598 1.0000 1.0000 XRAY> XRAY> do (map_fom=mod_fom) (all) XSFAL: allocating space for real reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> do (map_scale=distribute(mod_dd)) (all_active=1) XSFAL: allocating space for real reciprocal space object. Total of 10271 structure factor elements were selected. XRAY> XRAY> undeclare name=m domain=reciprocal end Object M has been undeclared. XRAY> undeclare name=mod_fom domain=reciprocal end Object MOD_FOM has been undeclared. XRAY> undeclare name=mod_x domain=reciprocal end Object MOD_X has been undeclared. XRAY> undeclare name=mod_pa domain=reciprocal end Object MOD_PA has been undeclared. XRAY> undeclare name=mod_pb domain=reciprocal end Object MOD_PB has been undeclared. XRAY> undeclare name=mod_pc domain=reciprocal end Object MOD_PC has been undeclared. XRAY> undeclare name=mod_pd domain=reciprocal end Object MOD_PD has been undeclared. XRAY> undeclare name=mod_dd domain=reciprocal end Object MOD_DD has been undeclared. XRAY> XRAY> end CNSsolve> CNSsolve> elseif ( &map_type = "combined" ) then CNSsolve> CNSsolve> xray CNSsolve> declare name=m domain=reciprocal type=complex end CNSsolve> declare name=mod_fom domain=reciprocal type=real end CNSsolve> declare name=mod_x domain=reciprocal type=real end CNSsolve> declare name=mod_pa domain=reciprocal type=real end CNSsolve> declare name=mod_pb domain=reciprocal type=real end CNSsolve> declare name=mod_pc domain=reciprocal type=real end CNSsolve> declare name=mod_pd domain=reciprocal type=real end CNSsolve> declare name=mod_dd domain=reciprocal type=real end CNSsolve> CNSsolve> @CNS_XTALMODULE:fomsigmaacv ( sig_sigacv=0.07; ASSFIL: file /sw/share/xtal/cns_solve_1.1/modules/xtal/fomsigmaacv opened. CNSsolve>! Module file: fom_sigmaacv CNSsolve>! CNSsolve>! CNS module CNSsolve>! ********** CNSsolve>! CNSsolve>! Authors: Axel Brunger and Paul Adams CNSsolve>! CNSsolve>! copyright Yale University CNSsolve>! CNSsolve>! Function: CNSsolve>! Calculates FOM from cross-validated sigmaa estimates CNSsolve>! CNSsolve>! Requirements: CNSsolve>! Needs to be called within xray CNSsolve> CNSsolve>module {fomsigmaacv} MODULE-DECLARATION> MODULE-DECLARATION>( MODULE-DECLARATION> &sig_sigacv=0.07; {real} MODULE-DECLARATION> &mbins=10; {real} MODULE-DECLARATION> &statistics=false; {logical} MODULE-DECLARATION> &fobs=fobs; {string} MODULE-DECLARATION> &fcalc=fcalc; {string} MODULE-DECLARATION> &fpart=fpart; {string} MODULE-DECLARATION> &test=test; {string} MODULE-DECLARATION> &sel=(all); {selection} MODULE-DECLARATION> &sel_test=none; {selection} MODULE-DECLARATION> &fom=fom; {string} MODULE-DECLARATION> &x=x; {string} MODULE-DECLARATION> &pa=pa; {string} MODULE-DECLARATION> &pb=pb; {string} MODULE-DECLARATION> &pc=pc; {string} MODULE-DECLARATION> &pd=pd; {string} MODULE-DECLARATION> &dd=dd; {string} MODULE-DECLARATION>) MODULE-INVOCATION> mbins=&target_bins; MODULE-INVOCATION> statistics=true; MODULE-INVOCATION> fobs=&STRIP%obs_f; MODULE-INVOCATION> fcalc=fcalc; MODULE-INVOCATION> fpart=fbulk; MODULE-INVOCATION> test=tst_active; MODULE-INVOCATION> sel=(map_active=1); MODULE-INVOCATION> sel_test=(tst_active=1); MODULE-INVOCATION> fom=mod_fom; MODULE-INVOCATION> x=mod_x; MODULE-INVOCATION> pa=mod_pa; MODULE-INVOCATION> pb=mod_pb; MODULE-INVOCATION> pc=mod_pc; MODULE-INVOCATION> pd=mod_pd; MODULE-INVOCATION> dd=mod_dd; ) CNSsolve> CNSsolve>set message ? end CNSsolve>evaluate ($message_old=$result) CNSsolve>set echo ? end CNSsolve>evaluate ($echo_old=$result) CNSsolve>if ( $log_level = verbose ) then CNSsolve> set echo=on message=normal end CNSsolve>else CNSsolve> set echo=off message=off end CNSsolve>end if CNSsolve> CNSsolve>checkversion 1.1 CNSsolve> CNSsolve>declare name=x_test domain=reciprocal type=real end CNSsolve>declare name=x_eobs domain=reciprocal type=real end CNSsolve>declare name=x_ecalc domain=reciprocal type=real end CNSsolve>declare name=x_sigmaa domain=reciprocal type=real end CNSsolve> CNSsolve>do (x_test=0) ( all ) CNSsolve>do (x_test=1) ( &sel_test ) CNSsolve> CNSsolve>show sum (1) (&sel_test) CNSsolve>if ( $result > 0 ) then CNSsolve> evaluate ($test_exist=true) CNSsolve> evaluate ($x_ntest=$result) CNSsolve>else CNSsolve> evaluate ($test_exist=false) CNSsolve> display Warning: no reflections flagged for cross-validation CNSsolve> display sigmaA estimates will not use cross-validation CNSsolve>end if CNSsolve> CNSsolve>{- Calculate number of bins used for E and x_sigmaa calculation. CNSsolve> Make sure there are at least 50 reflections in each bin. CNSsolve> Issue warning if there end up being less than 50 per bin -} CNSsolve>evaluate ($x_mbins=&mbins) CNSsolve>if ( &mbins < 0 ) then CNSsolve> if ( $test_exist = true ) then CNSsolve> show sum (1) (&sel_test) CNSsolve> else CNSsolve> show sum (1) (&sel) CNSsolve> end if CNSsolve> evaluate ($x_mbins=int($result/50)) CNSsolve> if ( $test_exist = true ) then CNSsolve> if ( $x_mbins <= 0 ) then CNSsolve> display Error: there are less than 50 test set reflections CNSsolve> display please check the test set and the resolution limits CNSsolve> abort CNSsolve> end if CNSsolve> if ( $x_mbins < 8 ) then CNSsolve> display Warning: there are less than 50 reflections per bin CNSsolve> display you may want to increase the size of the test set CNSsolve> end if CNSsolve> end if CNSsolve> evaluate ($x_mbins=max(8,$x_mbins)) CNSsolve> evaluate ($x_mbins=min($x_mbins,50)) CNSsolve>end if CNSsolve>mbins=$x_mbins CNSsolve> CNSsolve>{- Check to see that there are not too many bins with no CNSsolve> test set reflections - limit is 1/5th of total bins -} CNSsolve>if ($test_exist=true) then CNSsolve> declare name=x_temp domain=reciprocal type=real end CNSsolve> do (x_temp=sum(x_test)) ( &sel ) CNSsolve> show sum (1) ( &sel ) CNSsolve> evaluate ($ref_per_bin=$select/&mbins) CNSsolve> show sum (1) ( &sel and x_temp=0 ) CNSsolve> evaluate ($empty_bins=int($select/$ref_per_bin)) CNSsolve> undeclare name=x_temp domain=reciprocal end CNSsolve> evaluate ($empty_ratio=$empty_bins/&mbins) CNSsolve> if ( $empty_ratio >= 0.2 ) then CNSsolve> display Target-error: too many bins with no test set reflections CNSsolve> display test set must be randomly distributed CNSsolve> abort CNSsolve> end if CNSsolve>end if CNSsolve> CNSsolve>if ($test_exist=true) then CNSsolve> if ( $x_ntest < 400 ) then CNSsolve> do (x_eobs=norm(amplitude(&fobs))) ( &sel ) CNSsolve> do (x_ecalc=norm(amplitude(&fcalc+&fpart))) ( &sel ) CNSsolve> else CNSsolve> do (x_eobs=norm(amplitude(&fobs))) ( &sel_test ) CNSsolve> do (x_ecalc=norm(amplitude(&fcalc+&fpart))) ( &sel_test ) CNSsolve> end if CNSsolve> do (x_sigmaa=sigacv[sigma=&sig_sigacv](x_eobs,x_ecalc)) ( &sel_test ) CNSsolve> {- compute d -} CNSsolve> do (&dd=0) ( all ) CNSsolve> do (&dd= x_sigmaa * sqrt( save(amplitude(&fobs)^2) / CNSsolve> save(amplitude(&fcalc+&fpart)^2) ) ) ( &sel_test ) CNSsolve> {- Cross-validation active: need to expand to all selected CNSsolve> reflections and compute the normalized structure factor CNSsolve> for all data. -} CNSsolve> do (x_sigmaa=distribute(x_sigmaa)) ( &sel ) CNSsolve> do (&dd=distribute(&dd)) ( &sel ) CNSsolve> do (x_eobs=norm(amplitude(&fobs))) ( &sel ) CNSsolve> do (x_ecalc=norm(amplitude(&fcalc+&fpart))) ( &sel ) CNSsolve>else CNSsolve> do (x_eobs=norm(amplitude(&fobs))) ( &sel ) CNSsolve> do (x_ecalc=norm(amplitude(&fcalc+&fpart))) ( &sel ) CNSsolve> do (x_sigmaa=siga(x_eobs,x_ecalc)) ( &sel ) CNSsolve> {- compute d -} CNSsolve> do (&dd= x_sigmaa * sqrt( save(amplitude(&fobs)^2) / CNSsolve> save(amplitude(&fcalc+&fpart)^2) ) ) ( &sel ) CNSsolve>end if CNSsolve> CNSsolve>do (&x=2 x_sigmaa x_eobs x_ecalc / (1 - x_sigmaa^2)) ( &sel ) CNSsolve> CNSsolve>do (&pa=&x*cos(phase(&fcalc+&fpart))) ( &sel ) CNSsolve> CNSsolve>do (&pb=&x*sin(phase(&fcalc+&fpart))) ( &sel ) CNSsolve> CNSsolve>do (&pc=0) ( &sel ) CNSsolve>do (&pd=0) ( &sel ) CNSsolve> CNSsolve>do (&fom=i1overi0(&x)) ( acentric and &sel ) CNSsolve>do (&fom=tanh(&x/2)) ( centric and &sel ) CNSsolve> CNSsolve>if ( &statistics = true ) then CNSsolve> statistics CNSsolve> (&fom) (x_sigmaa) (&dd) (save(x_eobs^2)) (save(x_ecalc^2)) CNSsolve> selection=( &sel ) CNSsolve> end CNSsolve>end if CNSsolve> CNSsolve>undeclare name=x_eobs domain=reciprocal end CNSsolve>undeclare name=x_ecalc domain=reciprocal end CNSsolve>undeclare name=x_sigmaa domain=reciprocal end CNSsolve>undeclare name=x_test domain=reciprocal end CNSsolve> CNSsolve>set message=$message_old echo=$echo_old end CNSsolve> CNSsolve> @CNS_XTALMODULE:combineprobability ( messages="off"; ASSFIL: file /sw/share/xtal/cns_solve_1.1/modules/xtal/combineprobability opened. CNSsolve>! Module file: combineprobability CNSsolve>! CNSsolve>! CNS module CNSsolve>! ************ CNSsolve>! CNSsolve>! Authors: Piet Gros and Axel T. Brunger CNSsolve>! CNSsolve>! copyright Yale University CNSsolve>! CNSsolve>! Function: CNSsolve>! Combine phase probabilities from two different sources. CNSsolve>! CNSsolve>! Requirements: CNSsolve>! 1. This module can only be called called from xray CNSsolve>! 2. Probabilities have to be expressed in HL coefficients CNSsolve>! CNSsolve> CNSsolve>module {combineprobability} MODULE-DECLARATION>( MODULE-DECLARATION> &messages="normal"; {set verbosity "normal" | "all" | "off"} MODULE-DECLARATION> MODULE-DECLARATION> &sel=(all); {selection of reflections} MODULE-DECLARATION> MODULE-DECLARATION> &name="1"; {identifying text for probability} MODULE-DECLARATION> &w=1; {relative weight of phase probability} MODULE-DECLARATION> &pa=pa; {Hendrickson and Lattman A array} MODULE-DECLARATION> &pb=pb; {Hendrickson and Lattman B array} MODULE-DECLARATION> &pc=pc; {Hendrickson and Lattman C array} MODULE-DECLARATION> &pd=pd; {Hendrickson and Lattman D array} MODULE-DECLARATION> MODULE-DECLARATION> {Phase probability that will be added:} MODULE-DECLARATION> &addname="2"; {identifying text for probability that will be added} MODULE-DECLARATION> &addw=1; {relative weight of phase probability} MODULE-DECLARATION> &adda=null; {Hendrickson and Lattman A array} MODULE-DECLARATION> &addb=null; {Hendrickson and Lattman B array} MODULE-DECLARATION> &addc=null; {Hendrickson and Lattman C array} MODULE-DECLARATION> &addd=null; {Hendrickson and Lattman D array} MODULE-DECLARATION>) MODULE-INVOCATION> addname="model phases"; MODULE-INVOCATION> pa=mod_pa; MODULE-INVOCATION> pb=mod_pb; MODULE-INVOCATION> pc=mod_pc; MODULE-INVOCATION> pd=mod_pd; MODULE-INVOCATION> w=1; MODULE-INVOCATION> addname="experimental phases"; MODULE-INVOCATION> adda=&STRIP%obs_pa; MODULE-INVOCATION> addb=&STRIP%obs_pb; MODULE-INVOCATION> addc=&STRIP%obs_pc; MODULE-INVOCATION> addd=&STRIP%obs_pd; MODULE-INVOCATION> addw=1;) CNSsolve> CNSsolve>checkversion 1.1 CNSsolve> CNSsolve>if (&messages # "off") then CNSsolve> display COMBINEPROBABILITY: adding probability &name and &addname CNSsolve> display COMBINEPROBABILITY: P'(&name) = P(&name)^&w * P(&addname)^&addw CNSsolve>end if CNSsolve> CNSsolve>do (&pa=&w*&pa+&addw*&adda) (&sel) CNSsolve>do (&pb=&w*&pb+&addw*&addb) (&sel) CNSsolve>do (&pc=&w*&pc+&addw*&addc) (&sel) CNSsolve>do (&pd=&w*&pd+&addw*&addd) (&sel) CNSsolve> CNSsolve> CNSsolve> CNSsolve> @CNS_XTALMODULE:getfom ( pa=mod_pa; ASSFIL: file /sw/share/xtal/cns_solve_1.1/modules/xtal/getfom opened. CNSsolve>! Module file: getfom CNSsolve>! CNSsolve>! CNS module CNSsolve>! ********** CNSsolve>! CNSsolve>! Authors: Piet Gros and Axel T. Brunger CNSsolve>! CNSsolve>! copyright Yale University CNSsolve>! CNSsolve>! Function: CNSsolve>! Compute M: complex structure factor, amplitude: figure of merit and CNSsolve>! phase: centroid phase. CNSsolve>! CNSsolve>! Requirements: CNSsolve>! 1. This module can only be called from xray CNSsolve>! 2. Probability must be precomputed, supplied in Hendrickson & Lattman CNSsolve>! coefficients CNSsolve>! CNSsolve> CNSsolve>module {getfom} MODULE-DECLARATION>( MODULE-DECLARATION> &pa=pa; {Hendrickson and Lattman A array} MODULE-DECLARATION> &pb=pb; {Hendrickson and Lattman B array} MODULE-DECLARATION> &pc=pc; {Hendrickson and Lattman C array} MODULE-DECLARATION> &pd=pd; {Hendrickson and Lattman D array} MODULE-DECLARATION> MODULE-DECLARATION> &m=m; {complex: amplitude: figure-of-merit, phase: centroid phase} MODULE-DECLARATION> MODULE-DECLARATION> &sel=(all); {structure factor selection} MODULE-DECLARATION> MODULE-DECLARATION> &phistep=20; {size of phase steps in integration} MODULE-DECLARATION> &cen360=FALSE; { TRUE | FALSE (type logical); if TRUE a full 0...360 phase prob. distr. } MODULE-DECLARATION> { is used for centric reflections (useful if the "native" } MODULE-DECLARATION> { structure factor has an anomalous signal). } MODULE-DECLARATION>) MODULE-INVOCATION> pb=mod_pb; MODULE-INVOCATION> pc=mod_pc; MODULE-INVOCATION> pd=mod_pd; MODULE-INVOCATION> m=m; MODULE-INVOCATION> phistep=5; ) CNSsolve> CNSsolve>checkversion 1.1 CNSsolve> CNSsolve>do (&m=get_fom[phistep=&phistep,CEN360=&cen360](&pa,&pb,&pc,&pd) ) ( &sel ) CNSsolve> CNSsolve>! CNSsolve>! {*normalize probability*} CNSsolve>! CNSsolve>!@@normalizeprobability CNSsolve>! ( CNSsolve>! sel=sel; CNSsolve>! pk=pk; CNSsolve>! pa=pa;pb=pb;pc=pc;pd=pd; CNSsolve>! phistep=phistep; CNSsolve>! cen360=&cen360; CNSsolve>! ) CNSsolve>! CNSsolve>! {*compute complex fom*} CNSsolve>! CNSsolve>!do (m= CNSsolve>! (combine(1,centric_phase)* CNSsolve>! ( CNSsolve>! exp CNSsolve>! ( CNSsolve>! pk+pa*cos(centric_phase)+pb*sin(centric_phase) CNSsolve>! ) CNSsolve>! -exp CNSsolve>! ( CNSsolve>! pk-pa*cos(centric_phase)-pb*sin(centric_phase) CNSsolve>! ) CNSsolve>! ) CNSsolve>! ) CNSsolve>! ) ( (not &cen360) and centric and sel) CNSsolve>! CNSsolve>!do (m= CNSsolve>! (integrate[_phi,0,360,phistep] CNSsolve>! (combine(1,_phi)* CNSsolve>! exp CNSsolve>! ( CNSsolve>! pk+pa*cos(_phi)+pb*sin(_phi)+pc*cos(2*_phi)+pd*sin(2*_phi) CNSsolve>! ) CNSsolve>! ) CNSsolve>! ) CNSsolve>! ) (( &cen360 or acentric) and sel) CNSsolve>! CNSsolve>! CNSsolve>! CNSsolve> CNSsolve> do (map_phase=phase(m)) (all) CNSsolve> do (map_fom=amplitude(m)) (all) CNSsolve> do (map_scale=distribute(mod_dd)) (all_active=1) CNSsolve> CNSsolve> undeclare name=m domain=reciprocal end CNSsolve> undeclare name=mod_fom domain=reciprocal end CNSsolve> undeclare name=mod_x domain=reciprocal end CNSsolve> undeclare name=mod_pa domain=reciprocal end CNSsolve> undeclare name=mod_pb domain=reciprocal end CNSsolve> undeclare name=mod_pc domain=reciprocal end CNSsolve> undeclare name=mod_pd domain=reciprocal end CNSsolve> undeclare name=mod_dd domain=reciprocal end CNSsolve> end CNSsolve> CNSsolve> elseif ( &map_type = "observed" ) then CNSsolve> CNSsolve> xray CNSsolve> CNSsolve> do (total=fcalc+fbulk) (all) CNSsolve> multiscale CNSsolve> bfmin=-40 bfmax=40 CNSsolve> set1=&STRIP%obs_f k1=-1 b1=0 CNSsolve> set2=total b2=0 CNSsolve> selection=(map_active=1 and d <= &low_res_bscale) CNSsolve> end CNSsolve> do (map_scale=$k2) (all) CNSsolve> CNSsolve> declare name=m domain=reciprocal type=complex end CNSsolve> CNSsolve> @CNS_XTALMODULE:getfom ( pa=&STRIP%obs_pa; ASSFIL: file /sw/share/xtal/cns_solve_1.1/modules/xtal/getfom opened. CNSsolve>! Module file: getfom CNSsolve>! CNSsolve>! CNS module CNSsolve>! ********** CNSsolve>! CNSsolve>! Authors: Piet Gros and Axel T. Brunger CNSsolve>! CNSsolve>! copyright Yale University CNSsolve>! CNSsolve>! Function: CNSsolve>! Compute M: complex structure factor, amplitude: figure of merit and CNSsolve>! phase: centroid phase. CNSsolve>! CNSsolve>! Requirements: CNSsolve>! 1. This module can only be called from xray CNSsolve>! 2. Probability must be precomputed, supplied in Hendrickson & Lattman CNSsolve>! coefficients CNSsolve>! CNSsolve> CNSsolve>module {getfom} MODULE-DECLARATION>( MODULE-DECLARATION> &pa=pa; {Hendrickson and Lattman A array} MODULE-DECLARATION> &pb=pb; {Hendrickson and Lattman B array} MODULE-DECLARATION> &pc=pc; {Hendrickson and Lattman C array} MODULE-DECLARATION> &pd=pd; {Hendrickson and Lattman D array} MODULE-DECLARATION> MODULE-DECLARATION> &m=m; {complex: amplitude: figure-of-merit, phase: centroid phase} MODULE-DECLARATION> MODULE-DECLARATION> &sel=(all); {structure factor selection} MODULE-DECLARATION> MODULE-DECLARATION> &phistep=20; {size of phase steps in integration} MODULE-DECLARATION> &cen360=FALSE; { TRUE | FALSE (type logical); if TRUE a full 0...360 phase prob. distr. } MODULE-DECLARATION> { is used for centric reflections (useful if the "native" } MODULE-DECLARATION> { structure factor has an anomalous signal). } MODULE-DECLARATION>) MODULE-INVOCATION> pb=&STRIP%obs_pb; MODULE-INVOCATION> pc=&STRIP%obs_pc; MODULE-INVOCATION> pd=&STRIP%obs_pd; MODULE-INVOCATION> m=m; MODULE-INVOCATION> phistep=5; ) CNSsolve> CNSsolve>checkversion 1.1 CNSsolve> CNSsolve>do (&m=get_fom[phistep=&phistep,CEN360=&cen360](&pa,&pb,&pc,&pd) ) ( &sel ) CNSsolve> CNSsolve>! CNSsolve>! {*normalize probability*} CNSsolve>! CNSsolve>!@@normalizeprobability CNSsolve>! ( CNSsolve>! sel=sel; CNSsolve>! pk=pk; CNSsolve>! pa=pa;pb=pb;pc=pc;pd=pd; CNSsolve>! phistep=phistep; CNSsolve>! cen360=&cen360; CNSsolve>! ) CNSsolve>! CNSsolve>! {*compute complex fom*} CNSsolve>! CNSsolve>!do (m= CNSsolve>! (combine(1,centric_phase)* CNSsolve>! ( CNSsolve>! exp CNSsolve>! ( CNSsolve>! pk+pa*cos(centric_phase)+pb*sin(centric_phase) CNSsolve>! ) CNSsolve>! -exp CNSsolve>! ( CNSsolve>! pk-pa*cos(centric_phase)-pb*sin(centric_phase) CNSsolve>! ) CNSsolve>! ) CNSsolve>! ) CNSsolve>! ) ( (not &cen360) and centric and sel) CNSsolve>! CNSsolve>!do (m= CNSsolve>! (integrate[_phi,0,360,phistep] CNSsolve>! (combine(1,_phi)* CNSsolve>! exp CNSsolve>! ( CNSsolve>! pk+pa*cos(_phi)+pb*sin(_phi)+pc*cos(2*_phi)+pd*sin(2*_phi) CNSsolve>! ) CNSsolve>! ) CNSsolve>! ) CNSsolve>! ) (( &cen360 or acentric) and sel) CNSsolve>! CNSsolve>! CNSsolve>! CNSsolve> CNSsolve> do (map_phase=phase(m)) (all) CNSsolve> do (map_fom=amplitude(m)) (all) CNSsolve> do (map_scale=map_scale*map_fom) (all) CNSsolve> undeclare name=m domain=reciprocal end CNSsolve> end CNSsolve> CNSsolve> end if CNSsolve> CNSsolve> if ( &map_type = "gradient" ) then NEXTCD: condition evaluated as false CNSsolve> CNSsolve> xray CNSsolve> declare name=map domain=real end CNSsolve> {- take the negative of the gradient so the map is the same sign CNSsolve> as a standard difference map -} CNSsolve> do (map=ft(-dave)) (map_active=1) CNSsolve> end CNSsolve> CNSsolve> else CNSsolve> CNSsolve> xray XRAY> if ( &u = &v ) then NEXTCD: condition evaluated as false XRAY> do (fmap= 2 ((&u map_fom combine(amplitude(&STRIP%obs_f),map_phase)) - XRAY> (&v map_scale (fcalc+fbulk)))) XRAY> (map_active=1 and acentric) XRAY> do (fmap= (&u map_fom combine(amplitude(&STRIP%obs_f),map_phase)) - XRAY> (&v map_scale (fcalc+fbulk))) XRAY> (map_active=1 and centric) XRAY> else XRAY> do (fmap=(&u map_fom combine(amplitude(&STRIP%obs_f),map_phase)) - DO> (&v map_scale (fcalc+fbulk))) DO> (map_active=1 and acentric) XSFAL: allocating space for complex reciprocal space object. Total of 9147 structure factor elements were selected. XRAY> do (fmap=(max((&u-1),0) map_fom combine(amplitude(&STRIP%obs_f),map_phase)) - DO> (max((&v-1),0) map_scale (fcalc+fbulk))) DO> (map_active=1 and centric) Total of 388 structure factor elements were selected. XRAY> if ( &fill_in = true ) then NEXTCD: condition evaluated as false XRAY> do (fmap=(&u-&v) map_scale (fcalc+fbulk)) XRAY> ( all_active=1 and map_active # 1) XRAY> end if XRAY> end if XRAY> end CNSsolve> CNSsolve> xray XRAY> declare name=map domain=real end XRAY> if ( &u = &v ) then NEXTCD: condition evaluated as false XRAY> do (map=ft(fmap)) ( map_active=1 ) XRAY> else XRAY> if ( &fill_in = true ) then NEXTCD: condition evaluated as false XRAY> do (map=ft(fmap)) ( all_active=1 ) XRAY> else XRAY> do (map=ft(fmap)) ( map_active=1 ) XSFAL: allocating space for complex reciprocal space object. Total of 9535 structure factor elements were selected. XMAPAL: allocating space for real space object. XRAY> end if XRAY> end if XRAY> end CNSsolve> CNSsolve> end if CNSsolve> CNSsolve> if ( &write_coeff = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($coeff_out=&output_root + ".coeff") CNSsolve> xray CNSsolve> declare name=map_coeff domain=reciprocal type=complex end CNSsolve> do (map_coeff=fmap) (all) CNSsolve> write reflection CNSsolve> output=$coeff_out CNSsolve> if ( &map_type = "gradient" ) then CNSsolve> sele=(map_active=1) CNSsolve> elseif ( &fill_in = true ) then CNSsolve> sele=(&low_res >= d >= &high_res) CNSsolve> else CNSsolve> sele=(map_active=1) CNSsolve> end if CNSsolve> map_fom map_phase map_scale map_coeff CNSsolve> end CNSsolve> undeclare name=map_coeff domain=reciprocal end CNSsolve> end CNSsolve> end if CNSsolve> CNSsolve> xray XRAY> undeclare name=map_phase domain=reciprocal end Object MAP_PHASE has been undeclared. XRAY> undeclare name=map_fom domain=reciprocal end Object MAP_FOM has been undeclared. XRAY> undeclare name=map_scale domain=reciprocal end Object MAP_SCALE has been undeclared. XRAY> end CNSsolve> CNSsolve> xray XRAY> undeclare name=dtarg domain=reciprocal end Object DTARG has been undeclared. XRAY> undeclare name=fcave domain=reciprocal end Object FCAVE has been undeclared. XRAY> undeclare name=fpave domain=reciprocal end Object FPAVE has been undeclared. XRAY> undeclare name=foave domain=reciprocal end Object FOAVE has been undeclared. XRAY> undeclare name=dave domain=reciprocal end Object DAVE has been undeclared. XRAY> undeclare name=total domain=reciprocal end Object TOTAL has been undeclared. XRAY> undeclare name=fmap domain=reciprocal end Object FMAP has been undeclared. XRAY> end CNSsolve> CNSsolve> set remarks=reset end CNSsolve> set remarks=accumulate end CNSsolve> CNSsolve> xray XRAY> show sum (1) (tst_active=1) Sum of 959 elements = 959.0000 XRAY> if ( $result > 0 ) then NEXTCD: condition evaluated as true XRAY> evaluate ($test_exist=true) EVALUATE: symbol $TEST_EXIST set to TRUE (logical) XRAY> else XRAY> evaluate ($test_exist=false) XRAY> end if XRAY> end CNSsolve> CNSsolve> evaluate ($remark="") EVALUATE: symbol $REMARK set to "" (string) CNSsolve> if ( $struct > 1 ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($remark="averaged ") CNSsolve> end if CNSsolve> if ( &map_type = "unweighted" ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($remark=$remark + "(" + encode(&u) + " |Fo| - " + CNSsolve> encode(&v) + " k|Fc|)e^(i phi_calc)") CNSsolve> elseif ( &map_type = "sigmaa" ) then NEXTCD: condition evaluated as true CNSsolve> evaluate ($remark=$remark + "(" + encode(&u) + " m|Fo| - " + Expression= encode(&v) + " D|Fc|)e^(i phi_calc)") EVALUATE: symbol $REMARK set to "(2 m|Fo| - 1 D|Fc|)e^(i phi_calc)" (string) CNSsolve> if ( $test_exist = true ) then NEXTCD: condition evaluated as true CNSsolve> evaluate ($remark=$remark + " cross-val.") EVALUATE: symbol $REMARK set to "(2 m|Fo| - 1 D|Fc|)e^(i phi_calc) cross-val." (string) CNSsolve> end if CNSsolve> evaluate ($remark=$remark + " sigmaa") EVALUATE: symbol $REMARK set to "(2 m|Fo| - 1 D|Fc|)e^(i phi_calc) cross-val. sigmaa" (string) CNSsolve> elseif ( &map_type = "combined" ) then CNSsolve> evaluate ($remark=$remark + "(" + encode(&u) + " m|Fo|)e^(i phi_comb) - " + CNSsolve> "(" + encode(&v) + " D|Fc|)e^(i phi_calc)") CNSsolve> if ( $test_exist = true ) then CNSsolve> evaluate ($remark=$remark + " cross-val.") CNSsolve> end if CNSsolve> evaluate ($remark=$remark + " sigmaa") CNSsolve> elseif ( &map_type = "observed" ) then CNSsolve> evaluate ($remark=$remark + "(" + encode(&u) + " m|Fo|)e^(i phi_obs) - " + CNSsolve> "(" + encode(&v) + " k m|Fc|)e^(i phi_calc)") CNSsolve> elseif ( &map_type = "gradient" ) then CNSsolve> evaluate ($remark=$remark + "( d(" + &reftarget + ")/dFc )") CNSsolve> end if CNSsolve> CNSsolve> evaluate ($remark=$remark + " omit map") EVALUATE: symbol $REMARK set to "(2 m|Fo| - 1 D|Fc|)e^(i phi_calc) cross-val. sigmaa omit map" (string) CNSsolve> CNSsolve> if ( $total_test > 0 ) then NEXTCD: condition evaluated as true CNSsolve> remark $remark r= $map_r[f6.4] free_r= $map_free_r[f6.4] CNSsolve> else CNSsolve> remark $remark r= $map_r[f6.4] CNSsolve> end if CNSsolve> CNSsolve> if ( &obs_type = "intensity" ) then NEXTCD: condition evaluated as false CNSsolve> remark reflections with Iobs/sigma_I < &sigma_cut rejected CNSsolve> remark reflections with Iobs > &obs_rms * rms(Iobs) rejected CNSsolve> else CNSsolve> remark reflections with |Fobs|/sigma_F < &sigma_cut rejected CNSsolve> remark reflections with |Fobs| > &obs_rms * rms(Fobs) rejected CNSsolve> end if CNSsolve> xray anomalous=? end ANOMalous=FALSe {OFF} CNSsolve> if ( $result = true ) then NEXTCD: condition evaluated as false CNSsolve> remark anomalous diffraction data was input CNSsolve> end if CNSsolve> remark theoretical total number of refl. in resol. range: $total_theor[I6] ( 100.0 % ) CNSsolve> remark number of unobserved reflections (no entry or |F|=0): $unobserved[I6] ( $per_unobs[f5.1] % ) CNSsolve> remark number of reflections rejected: $rejected[I6] ( $per_reject[f5.1] % ) CNSsolve> remark total number of reflections used: $total_used[I6] ( $per_used[f5.1] % ) CNSsolve> remark number of reflections in working set: $total_work[I6] ( $per_work[f5.1] % ) CNSsolve> remark number of reflections in test set: $total_test[I6] ( $per_test[f5.1] % ) CNSsolve> CNSsolve> if ( &bulk_sol = true ) then NEXTCD: condition evaluated as true CNSsolve> remark bulk solvent: density level= $sol_k_ref e/A^3, B-factor= $sol_b_ref A^2 CNSsolve> else CNSsolve> remark bulk solvent: false CNSsolve> end if CNSsolve> CNSsolve> if ( &bscale # "no" ) then NEXTCD: condition evaluated as true CNSsolve> remark B-correction resolution: &low_res_bscale - &high_res CNSsolve> else CNSsolve> remark initial B-factor correction: none CNSsolve> end if CNSsolve> CNSsolve> if ( &bscale = "anisotropic" ) then NEXTCD: condition evaluated as true CNSsolve> remark initial B-factor correction applied to &STRIP%obs_f : CNSsolve> remark B11= $aniso_11 B22= $aniso_22 B33= $aniso_33 CNSsolve> remark B12= $aniso_12 B13= $aniso_13 B23= $aniso_23 CNSsolve> remark B-factor correction applied to coordinate array B: $trace[f8.3] CNSsolve> elseif ( &bscale = "anisotropic_fixed_anisotropic" ) then CNSsolve> remark initial B-factor correction applied to &STRIP%obs_f : CNSsolve> remark B11= $aniso_11 B22= $aniso_22 B33= $aniso_33 CNSsolve> remark B12= $aniso_12 B13= $aniso_13 B23= $aniso_23 CNSsolve> remark no B-factor correction applied to coordinate array B CNSsolve> elseif ( &bscale = "isotropic" ) then CNSsolve> remark B-factor correction applied to coordinate array B: $trace[f8.3] CNSsolve> end if CNSsolve> CNSsolve> if (&map_scale=true) then NEXTCD: condition evaluated as true CNSsolve> xray XRAY> show rms (real(map)) ( all ) Rms of 331776 elements = 0.2174 XRAY> do (map=map/$result) ( all ) Total of 331776 map elements were selected. XRAY> end CNSsolve> end if CNSsolve> CNSsolve> if ( &write_map = true ) then NEXTCD: condition evaluated as true CNSsolve> CNSsolve> evaluate ($map_outfile=&output_root + ".map") EVALUATE: symbol $MAP_OUTFILE set to "refine-0-2.map" (string) CNSsolve> CNSsolve> if ( &map_mode = "asymmetric" ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($map_mode_string=ASYM) CNSsolve> elseif ( &map_mode = "unit" ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($map_mode_string=UNIT) CNSsolve> elseif ( &map_mode = "box" ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($map_mode_string=BOX) CNSsolve> elseif ( &map_mode = "fract" ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($map_mode_string=FRAC) CNSsolve> else CNSsolve> evaluate ($map_mode_string=MOLE) Assuming literal string "MOLE" EVALUATE: symbol $MAP_MODE_STRING set to "MOLE" (string) CNSsolve> end if CNSsolve> xray XRAY> write map WRITe MAP> if ( &map_format = "ezd" ) then NEXTCD: condition evaluated as false WRITe MAP> type=ezd WRITe MAP> else WRITe MAP> type=cns WRITe MAP> end if WRITe MAP> automatic=false WRITe MAP> from=map WRITe MAP> output=$map_outfile WRITe MAP> cushion=&map_cushion WRITe MAP> selection=&atom_map SELRPN: 1275 atoms have been selected out of 1275 WRITe MAP> extend=$map_mode_string WRITe MAP> if ( &map_mode = "box" ) then NEXTCD: condition evaluated as false WRITe MAP> xmin=&xmin xmax=&xmax WRITe MAP> ymin=&ymin ymax=&ymax WRITe MAP> zmin=&zmin zmax=&zmax WRITe MAP> end if WRITe MAP> if ( &map_mode = "fract" ) then NEXTCD: condition evaluated as false WRITe MAP> xmin=&xmin xmax=&xmax WRITe MAP> ymin=&ymin ymax=&ymax WRITe MAP> zmin=&zmin zmax=&zmax WRITe MAP> end if WRITe MAP> end ASSFIL: file refine-0-2.map opened. XMAPX: map will be written in [e]/A^3 units. XMAPX: extend NA=( 96 -65 25) NB=( 96 -15 66) NC=( 144 -50 45) XMAPX: ave. density (real) in unit cell= 0.00000 sigma= 1.00000 e/A^3 XMAPX: real part of section # 0 ave. dens.= -0.00016 sigma= 0.88648 e/A^3 XMAPX: real part of section # 1 ave. dens.= 0.00288 sigma= 0.89982 e/A^3 XMAPX: real part of section # 2 ave. dens.= -0.00680 sigma= 0.87134 e/A^3 XMAPX: real part of section # 3 ave. dens.= -0.00786 sigma= 0.85770 e/A^3 XMAPX: real part of section # 4 ave. dens.= 0.00651 sigma= 0.88892 e/A^3 XMAPX: real part of section # 5 ave. dens.= 0.02398 sigma= 0.90181 e/A^3 XMAPX: real part of section # 6 ave. dens.= 0.03068 sigma= 0.88493 e/A^3 XMAPX: real part of section # 7 ave. dens.= 0.02572 sigma= 0.88701 e/A^3 XMAPX: real part of section # 8 ave. dens.= 0.01664 sigma= 0.88537 e/A^3 XMAPX: real part of section # 9 ave. dens.= 0.00768 sigma= 0.85665 e/A^3 XMAPX: real part of section # 10 ave. dens.= -0.00114 sigma= 0.85313 e/A^3 XMAPX: real part of section # 11 ave. dens.= -0.00646 sigma= 0.89425 e/A^3 XMAPX: real part of section # 12 ave. dens.= -0.00121 sigma= 0.93089 e/A^3 XMAPX: real part of section # 13 ave. dens.= 0.01559 sigma= 0.94169 e/A^3 XMAPX: real part of section # 14 ave. dens.= 0.03405 sigma= 0.94458 e/A^3 XMAPX: real part of section # 15 ave. dens.= 0.04261 sigma= 0.95611 e/A^3 XMAPX: real part of section # 16 ave. dens.= 0.04003 sigma= 0.98225 e/A^3 XMAPX: real part of section # 17 ave. dens.= 0.03415 sigma= 1.01291 e/A^3 XMAPX: real part of section # 18 ave. dens.= 0.02976 sigma= 1.02913 e/A^3 XMAPX: real part of section # 19 ave. dens.= 0.02266 sigma= 1.00976 e/A^3 XMAPX: real part of section # 20 ave. dens.= 0.00835 sigma= 0.95805 e/A^3 XMAPX: real part of section # 21 ave. dens.= -0.00624 sigma= 0.92526 e/A^3 XMAPX: real part of section # 22 ave. dens.= -0.00484 sigma= 0.95229 e/A^3 XMAPX: real part of section # 23 ave. dens.= 0.02088 sigma= 1.00749 e/A^3 XMAPX: real part of section # 24 ave. dens.= 0.05683 sigma= 1.04959 e/A^3 XMAPX: real part of section # 25 ave. dens.= 0.07421 sigma= 1.07803 e/A^3 XMAPX: real part of section # 26 ave. dens.= 0.05682 sigma= 1.08876 e/A^3 XMAPX: real part of section # 27 ave. dens.= 0.02056 sigma= 1.07771 e/A^3 XMAPX: real part of section # 28 ave. dens.= -0.00024 sigma= 1.07276 e/A^3 XMAPX: real part of section # 29 ave. dens.= 0.01003 sigma= 1.10030 e/A^3 XMAPX: real part of section # 30 ave. dens.= 0.02907 sigma= 1.13216 e/A^3 XMAPX: real part of section # 31 ave. dens.= 0.02184 sigma= 1.11655 e/A^3 XMAPX: real part of section # 32 ave. dens.= -0.01714 sigma= 1.06232 e/A^3 XMAPX: real part of section # 33 ave. dens.= -0.05632 sigma= 1.02037 e/A^3 XMAPX: real part of section # 34 ave. dens.= -0.06560 sigma= 1.00601 e/A^3 XMAPX: real part of section # 35 ave. dens.= -0.05215 sigma= 1.01138 e/A^3 XMAPX: real part of section # 36 ave. dens.= -0.04753 sigma= 1.02876 e/A^3 XMAPX: real part of section # 37 ave. dens.= -0.06441 sigma= 1.02877 e/A^3 XMAPX: real part of section # 38 ave. dens.= -0.08099 sigma= 1.00590 e/A^3 XMAPX: real part of section # 39 ave. dens.= -0.07234 sigma= 1.00932 e/A^3 XMAPX: real part of section # 40 ave. dens.= -0.04442 sigma= 1.03520 e/A^3 XMAPX: real part of section # 41 ave. dens.= -0.02581 sigma= 1.02710 e/A^3 XMAPX: real part of section # 42 ave. dens.= -0.03200 sigma= 1.00746 e/A^3 XMAPX: real part of section # 43 ave. dens.= -0.05135 sigma= 1.01228 e/A^3 XMAPX: real part of section # 44 ave. dens.= -0.06620 sigma= 0.99494 e/A^3 XMAPX: real part of section # 45 ave. dens.= -0.07404 sigma= 0.95300 e/A^3 XMAPX: real part of section # 46 ave. dens.= -0.08038 sigma= 0.95895 e/A^3 XMAPX: real part of section # 47 ave. dens.= -0.08098 sigma= 1.00823 e/A^3 XMAPX: real part of section # 48 ave. dens.= -0.06506 sigma= 1.03800 e/A^3 XMAPX: real part of section # 49 ave. dens.= -0.03530 sigma= 1.04525 e/A^3 XMAPX: real part of section # 50 ave. dens.= -0.01150 sigma= 1.05408 e/A^3 XMAPX: real part of section # 51 ave. dens.= -0.00759 sigma= 1.06211 e/A^3 XMAPX: real part of section # 52 ave. dens.= -0.01215 sigma= 1.07164 e/A^3 XMAPX: real part of section # 53 ave. dens.= -0.00223 sigma= 1.10351 e/A^3 XMAPX: real part of section # 54 ave. dens.= 0.02430 sigma= 1.14332 e/A^3 XMAPX: real part of section # 55 ave. dens.= 0.04050 sigma= 1.13864 e/A^3 XMAPX: real part of section # 56 ave. dens.= 0.02142 sigma= 1.08185 e/A^3 XMAPX: real part of section # 57 ave. dens.= -0.02076 sigma= 1.02958 e/A^3 XMAPX: real part of section # 58 ave. dens.= -0.04288 sigma= 1.03624 e/A^3 XMAPX: real part of section # 59 ave. dens.= -0.01619 sigma= 1.08310 e/A^3 XMAPX: real part of section # 60 ave. dens.= 0.03979 sigma= 1.12163 e/A^3 XMAPX: real part of section # 61 ave. dens.= 0.07650 sigma= 1.14869 e/A^3 XMAPX: real part of section # 62 ave. dens.= 0.06886 sigma= 1.16169 e/A^3 XMAPX: real part of section # 63 ave. dens.= 0.04046 sigma= 1.15222 e/A^3 XMAPX: real part of section # 64 ave. dens.= 0.03171 sigma= 1.14588 e/A^3 XMAPX: real part of section # 65 ave. dens.= 0.04986 sigma= 1.16076 e/A^3 XMAPX: real part of section # 66 ave. dens.= 0.06178 sigma= 1.16625 e/A^3 XMAPX: real part of section # 67 ave. dens.= 0.03702 sigma= 1.13065 e/A^3 XMAPX: real part of section # 68 ave. dens.= -0.01365 sigma= 1.08256 e/A^3 XMAPX: real part of section # 69 ave. dens.= -0.05140 sigma= 1.06289 e/A^3 XMAPX: real part of section # 70 ave. dens.= -0.05516 sigma= 1.05160 e/A^3 XMAPX: real part of section # 71 ave. dens.= -0.04249 sigma= 1.03077 e/A^3 XMAPX: real part of section # 72 ave. dens.= -0.04285 sigma= 1.02633 e/A^3 XMAPX: real part of section # 73 ave. dens.= -0.06059 sigma= 1.02880 e/A^3 XMAPX: real part of section # 74 ave. dens.= -0.07257 sigma= 1.01085 e/A^3 XMAPX: real part of section # 75 ave. dens.= -0.05861 sigma= 1.00306 e/A^3 XMAPX: real part of section # 76 ave. dens.= -0.02478 sigma= 1.01448 e/A^3 XMAPX: real part of section # 77 ave. dens.= 0.00511 sigma= 1.00403 e/A^3 XMAPX: real part of section # 78 ave. dens.= 0.01431 sigma= 0.98741 e/A^3 XMAPX: real part of section # 79 ave. dens.= 0.00477 sigma= 0.98724 e/A^3 XMAPX: real part of section # 80 ave. dens.= -0.01180 sigma= 0.95999 e/A^3 XMAPX: real part of section # 81 ave. dens.= -0.02700 sigma= 0.91570 e/A^3 XMAPX: real part of section # 82 ave. dens.= -0.03771 sigma= 0.92411 e/A^3 XMAPX: real part of section # 83 ave. dens.= -0.04009 sigma= 0.96850 e/A^3 XMAPX: real part of section # 84 ave. dens.= -0.02893 sigma= 0.99032 e/A^3 XMAPX: real part of section # 85 ave. dens.= -0.00521 sigma= 0.99115 e/A^3 XMAPX: real part of section # 86 ave. dens.= 0.01962 sigma= 0.99578 e/A^3 XMAPX: real part of section # 87 ave. dens.= 0.03288 sigma= 1.00567 e/A^3 XMAPX: real part of section # 88 ave. dens.= 0.03463 sigma= 1.01599 e/A^3 XMAPX: real part of section # 89 ave. dens.= 0.03694 sigma= 1.04131 e/A^3 XMAPX: real part of section # 90 ave. dens.= 0.04546 sigma= 1.07685 e/A^3 XMAPX: real part of section # 91 ave. dens.= 0.04711 sigma= 1.06810 e/A^3 XMAPX: real part of section # 92 ave. dens.= 0.02520 sigma= 0.99487 e/A^3 XMAPX: real part of section # 93 ave. dens.= -0.01305 sigma= 0.92498 e/A^3 XMAPX: real part of section # 94 ave. dens.= -0.03512 sigma= 0.92923 e/A^3 XMAPX: real part of section # 95 ave. dens.= -0.01729 sigma= 0.97384 e/A^3 XRAY> end CNSsolve> end if CNSsolve> CNSsolve> if ( &peak_search = true ) then NEXTCD: condition evaluated as false CNSsolve> evaluate ($filename=&output_root + "_positive.peaks") CNSsolve> xray CNSsolve> peakpik CNSsolve> from=map CNSsolve> mpeak=&peak_num CNSsolve> selection=( all ) CNSsolve> atom=true CNSsolve> proximity=(&atom_map) CNSsolve> end CNSsolve> end CNSsolve> CNSsolve> write coor output=$filename selection=(segid=PEAK) end CNSsolve> CNSsolve> delete sele=(segid=PEAK) end CNSsolve> CNSsolve> evaluate ($filename=&output_root + "_negative.peaks") CNSsolve> xray CNSsolve> do (map=-map) ( all ) CNSsolve> peakpik CNSsolve> from=map CNSsolve> mpeak=&peak_num CNSsolve> selection=( all ) CNSsolve> atom=true CNSsolve> proximity=(&atom_map) CNSsolve> end CNSsolve> end CNSsolve> CNSsolve> write coor output=$filename selection=(segid=PEAK) end CNSsolve> end if CNSsolve> CNSsolve> stop ============================================================ Maximum dynamic memory allocation: 19692516 bytes Maximum dynamic memory overhead: 1456 bytes Program started at: 09:31:21 on 15-Sep-2005 Program stopped at: 09:36:10 on 15-Sep-2005 CPU time used: 263.9200 seconds ============================================================