ó әxTc@ sŚddlmZddlZddlZddlZdZdZdZ dd„Z e dkr˘xAd d gD]0Z x'd d gD]Z e d e de ƒq~WqkWndS(i˙˙˙˙(tdivisionNs‚ 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 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 0.01 15.00 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 0.01 15.00 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 0.01 15.00 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 0.01 15.00 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 0.91 15.00 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 0.91 15.00 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 0.91 15.00 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 0.91 15.00 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 0.91 15.00 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 0.91 15.00 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 0.91 15.00 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 0.91 15.00 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 0.00 15.00 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 0.00 15.00 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 0.00 15.00 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 0.00 15.00 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 0.00 15.00 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 0.00 15.00 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 0.00 15.00 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 0.00 15.00 N ATOM 21 N GLN A 4 -1.005 2.228 3.598 7.00 15.00 N ATOM 22 CA GLN A 4 0.384 1.888 3.199 7.00 15.00 C ATOM 23 C GLN A 4 1.435 2.606 4.088 7.00 15.00 C ATOM 24 O GLN A 4 1.547 3.843 4.115 7.00 15.00 O ATOM 25 CB GLN A 4 0.656 2.148 1.711 7.00 15.00 C ATOM 26 CG GLN A 4 1.944 1.458 1.213 7.00 15.00 C ATOM 27 CD GLN A 4 2.504 2.044 -0.089 7.00 15.00 C ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 7.00 15.00 O ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 7.00 15.00 N ATOM 30 N GLN A 5 2.154 1.821 4.871 0.01 15.00 N ATOM 31 CA GLN A 5 3.270 2.361 5.640 0.01 15.00 C ATOM 32 C GLN A 5 4.594 1.768 5.172 0.01 15.00 C ATOM 33 O GLN A 5 4.768 0.546 5.054 0.01 15.00 O ATOM 34 CB GLN A 5 3.056 2.183 7.147 0.01 15.00 C ATOM 35 CG GLN A 5 1.829 2.950 7.647 0.01 15.00 C ATOM 36 CD GLN A 5 1.344 2.414 8.954 0.01 15.00 C ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 0.01 15.00 O ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 0.01 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 5.00 15.00 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 5.00 15.00 C ATOM 49 C TYR A 7 10.603 2.331 6.885 5.00 15.00 C ATOM 50 O TYR A 7 11.041 1.811 5.855 5.00 15.00 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 5.00 15.00 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 5.00 15.00 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 5.00 15.00 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 5.00 15.00 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 5.00 15.00 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 5.00 15.00 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 5.00 15.00 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 5.00 15.00 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 5.00 15.00 O END icC sŇ|dkr!t}t}t}nt}t}t}tjjddd|ƒ}|jƒ}|j ƒj ƒ|j ƒ}tjjdddt ƒj ƒ} t | jddddƒjƒƒ} tjjjƒ} d| _tjjd| d |d | ƒ} | jƒ| jd |ƒd | jƒ| jƒfGHtjjd | ƒ} | jd|d|ƒ}x|D]}dt|ƒGHq`WH|jd|ƒ}|rčdGHtjj jd | d|dddddtdtdtdtddddƒ }n|r8d GHtjj jd | d|dddddtdtdtdtƒ}nd!| jƒ| jƒfGH|j!| j"ƒ|j#d"d#d$| j$ƒƒ|j%d%ks t&||gƒ‚| jƒd&}|d'ksÎt&||gƒ‚dS((Nt refine_adpt source_infotlinestd_minit algorithmtdirecttsf_and_grads_accuracy_paramstxray_structuretf_obst target_names!Initial r_work=%6.4f r_free=%6.4ftfmodelt pdb_hierarchytresidues_per_windows+chainID_resseqs: %s occupancy_grad: %-15.6ftresidues_per_chunksrefine occupancies:t selectionstmax_number_of_iterationsi2tnumber_of_macro_cyclesit refine_occtconvergence_testtuse_restraintstrun_finite_differences_testt occupancy_maxiçt occupancy_miniü˙˙srefine b-factorss*After refinement r_work=%6.4f r_free=%6.4ft file_namesrefined_occupancies.pdbtcrystal_symmetryiidgš™™™™™š?('tTruetFalsetpdb_poor_adp_strtpdb_poor_occ_strtiotbxtpdbtinputtNonetconstruct_hierarchytatomst reset_i_seqtxray_structure_simpletpdb_answer_strtabststructure_factorstf_calctmmtbxtf_modelt#sf_and_grads_accuracy_master_paramstextractRtmanagertshowtupdatetr_worktr_freetutilst&experimental_data_target_and_gradientstgroup_occupancy_gradsttupletchunk_selectionst refinementtgrouptadopt_xray_structureRtwrite_pdb_fileRttestedtAssertionError(trefinettargetR RRt pdb_poor_strt pdb_inp_poortphtxrs_poort xrs_answerR tsfpR ttgtresulttrRtrrR1((sH/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/tst_group.pytrunĆs~    $          !t__main__tmltls_wunit_kunitRRR>R?(t __future__Rt iotbx.pdbRt mmtbx.utilsR*tmmtbx.refinement.groupR&RRRJt__name__R?R>(((sH/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/tst_group.pyts   @@@ F