ó Ñ™xTc@ s…ddlmZddlZddlZddlZddlmZdZ dZ ddd„Z e d kre d d d d ƒndS(iÿÿÿÿ(tdivisionN(tmillers‚ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 15.00 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 15.00 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 15.00 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 15.00 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.00 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 15.00 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 15.00 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 15.00 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00 15.00 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00 15.00 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00 15.00 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 15.00 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 15.00 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 15.00 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 15.00 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 15.00 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 15.00 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 15.00 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 15.00 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 15.00 N ATOM 21 N GLN A 4 -1.005 2.228 3.598 1.00 15.00 N ATOM 22 CA GLN A 4 0.384 1.888 3.199 1.00 15.00 C ATOM 23 C GLN A 4 1.435 2.606 4.088 1.00 15.00 C ATOM 24 O GLN A 4 1.547 3.843 4.115 1.00 15.00 O ATOM 25 CB GLN A 4 0.656 2.148 1.711 1.00 15.00 C ATOM 26 CG GLN A 4 1.944 1.458 1.213 1.00 15.00 C ATOM 27 CD GLN A 4 2.504 2.044 -0.089 1.00 15.00 C ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 1.00 15.00 O ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 1.00 15.00 N ATOM 30 N GLN A 5 2.154 1.821 4.871 1.00 15.00 N ATOM 31 CA GLN A 5 3.270 2.361 5.640 1.00 15.00 C ATOM 32 C GLN A 5 4.594 1.768 5.172 1.00 15.00 C ATOM 33 O GLN A 5 4.768 0.546 5.054 1.00 15.00 O ATOM 34 CB GLN A 5 3.056 2.183 7.147 1.00 15.00 C ATOM 35 CG GLN A 5 1.829 2.950 7.647 1.00 15.00 C ATOM 36 CD GLN A 5 1.344 2.414 8.954 1.00 15.00 C ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 1.00 15.00 O ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 1.00 15.00 N ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 15.00 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 15.00 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 15.00 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 15.00 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 15.00 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 15.00 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 15.00 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 15.00 N ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 15.00 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.00 C ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.00 C ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.00 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.00 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 15.00 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.00 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 15.00 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 15.00 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 15.00 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.00 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 15.00 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 15.00 O END s‚ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 0.01 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 0.01 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 0.01 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 0.01 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00495.00 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00495.00 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00495.00 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00495.00 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00495.00 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00495.00 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00495.00 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00495.00 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 2.00 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 2.00 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 2.00 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 2.00 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 2.00 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 2.00 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 2.00 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 2.00 N ATOM 21 N GLN A 4 -1.005 2.228 3.598 1.00385.00 N ATOM 22 CA GLN A 4 0.384 1.888 3.199 1.00385.00 C ATOM 23 C GLN A 4 1.435 2.606 4.088 1.00385.00 C ATOM 24 O GLN A 4 1.547 3.843 4.115 1.00385.00 O ATOM 25 CB GLN A 4 0.656 2.148 1.711 1.00385.00 C ATOM 26 CG GLN A 4 1.944 1.458 1.213 1.00385.00 C ATOM 27 CD GLN A 4 2.504 2.044 -0.089 1.00385.00 C ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 1.00385.00 O ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 1.00385.00 N ATOM 30 N GLN A 5 2.154 1.821 4.871 1.00 0.03 N ATOM 31 CA GLN A 5 3.270 2.361 5.640 1.00 0.03 C ATOM 32 C GLN A 5 4.594 1.768 5.172 1.00 0.03 C ATOM 33 O GLN A 5 4.768 0.546 5.054 1.00 0.03 O ATOM 34 CB GLN A 5 3.056 2.183 7.147 1.00 0.03 C ATOM 35 CG GLN A 5 1.829 2.950 7.647 1.00 0.03 C ATOM 36 CD GLN A 5 1.344 2.414 8.954 1.00 0.03 C ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 1.00 0.03 O ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 1.00 0.03 N ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00290.00 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00290.00 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00290.00 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00290.00 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00290.00 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00290.00 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00290.00 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00290.00 N ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 0.00 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 0.00 C ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 0.00 C ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 0.00 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 0.00 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 0.00 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 0.00 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 0.00 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 0.00 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 0.00 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 0.00 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 0.00 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 0.00 O END iicC s¸tjjdd)dtƒ}|jddƒ|jƒ}|jƒjƒ|j ƒ}tjjdd)dt ƒj ƒ}|j d|ddƒj ƒ}|j dd ƒ} t|ƒ} |jd d ƒ} | jƒ| jƒ} tjd |jƒd td|ƒ} | jd| dtd tdtƒ}t|ƒ}| jd|ddƒ| jd|jƒddƒ| jƒ}|jddƒtjjjƒ}d|_ tjj!d|d|d|ƒ}|j"ƒ|j#d|ƒd|j$ƒ|j%ƒfGH|j&d|ƒ}tj'j(j!d|d|dddd d!td"td#td$tƒ}d%|j$ƒ|j%ƒfGH|j)|j*ƒ|jdd&d |jƒƒ|j$ƒd'}|d(ks´t+||gƒ‚d)S(*s& Makes sure this actually work: 'real-space' ADP refinement by converting the map into 'Fobs' and then actually doing usual reciprocal-space refinement. Surprisingly this converges to R=0 exactly regardless the resolution. ML does not work perhaps becase starting point is too far. t source_infotlinest file_namespoor.pdbtd_mint algorithmtdirecttcolumn_root_labelsF-calctresolution_factorgÐ?tcrystal_symmetrytanomalous_flagtmapt use_scaletuse_sgt miller_arraysF-obss R-free-flagssdata.mtztsf_and_grads_accuracy_paramstxray_structuretf_obst target_names!Initial r_work=%6.4f r_free=%6.4ftresidues_per_chunktfmodelt selectionstmax_number_of_iterationsi2tnumber_of_macro_cyclesitconvergence_testtrun_finite_differences_testt refine_adptuse_restraintss*After refinement r_work=%6.4f r_free=%6.4fs&reciprocal_space_refined_group_adp.pdbidgš™™™™™¹?N(,tiotbxtpdbtinputtNonetpdb_poor_adp_strtwrite_pdb_filetconstruct_hierarchytatomst reset_i_seqtxray_structure_simpletpdb_answer_strtstructure_factorstf_calctas_mtz_datasettabstfft_maptapply_volume_scalingtreal_map_unpaddedRt build_setR tFalsetstructure_factors_from_maptTruetadd_miller_arraytgenerate_r_free_flagst mtz_objecttwritetmmtbxtf_modelt#sf_and_grads_accuracy_master_paramstextractRtmanagertshowtupdatetr_worktr_freetchunk_selectionst refinementtgrouptadopt_xray_structureRtAssertionError(trefinettargettresidues_per_windowRt pdb_inp_poortphtxrs_poort xrs_answerRt mtz_datasettfcR,tmap_datat complete_setR5tsfpRRtrrR>((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/tst_group_2.pytrunˆsr                     t__main__RERRFt ls_wunit_k1( t __future__Rt iotbx.pdbRtmmtbx.refinement.groupR7t mmtbx.f_modeltcctbxRR'R!RRt__name__(((sJ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/tst_group_2.pyts   @@E