MODELLER 9.16, 2016/01/07, r10745 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2016 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux sunflower.rnet.missouri.edu 2.6.32-431.23.3.el6.x86_64 x86_64 Date and time of compilation : 2016/01/07 10:19:44 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2016/04/05 22:41:21 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v16}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v16}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191562 187.072 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192090 187.588 0.183 openf___224_> Open ${MODINSTALL9v16}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240690 235.049 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v16}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253990 248.037 0.242 openf___224_> Open ${MODINSTALL9v16}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v16}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v16}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v16}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open twochain.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 265439 259.218 0.253 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 266889 260.634 0.255 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269789 263.466 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 330673 322.923 0.315 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 330701 322.950 0.315 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 330729 322.978 0.315 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 331317 323.552 0.316 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 331905 324.126 0.317 Read the alignment from file : twochain.ali Total number of alignment positions: 148 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2abx 148 2 2abx bungarotoxin 2 1hc9 148 2 1hc9 undefined check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ../atom_files/pdb2abx.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 378030 369.170 0.361 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 378030 369.170 0.361 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 378201 369.337 0.361 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 379051 370.167 0.361 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 380309 371.396 0.363 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 382213 373.255 0.365 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 382213 373.255 0.365 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 382303 373.343 0.365 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 385159 376.132 0.367 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 385159 376.132 0.367 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 385294 376.264 0.367 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 389578 380.447 0.372 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 389578 380.447 0.372 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 389776 380.641 0.372 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 396202 386.916 0.378 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 396202 386.916 0.378 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 396499 387.206 0.378 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 396499 387.206 0.378 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 396499 387.206 0.378 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 406121 396.603 0.387 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406121 396.603 0.387 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 406571 397.042 0.388 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 421021 411.153 0.402 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 421003 411.136 0.401 check_ali___> Checking the sequence-structure alignment. Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE check_a_344_> << END OF COMMAND openf___224_> Open ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 560255 547.124 0.534 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 561855 548.687 0.536 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 565835 552.573 0.540 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 567835 554.526 0.542 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 570835 557.456 0.544 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 575335 561.851 0.549 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 580907 567.292 0.554 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 583707 570.026 0.557 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 587907 574.128 0.561 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 594207 580.280 0.567 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 596979 582.987 0.569 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 598379 584.354 0.571 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 609840 595.547 0.582 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 665798 650.193 0.635 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 673910 658.115 0.643 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 74 552 566 0 0 224 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 698178 681.814 0.666 patch_______> segment topology patched using RTF: 1 ; ILE ; NTER segments residues atoms bonds angles dihedrals impropers: 1 74 552 566 770 941 224 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 723978 707.010 0.690 patch_______> segment topology patched using RTF: 74 ; GLY ; CTER segments residues atoms bonds angles dihedrals impropers: 1 74 553 567 772 942 225 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 74 553 567 772 942 225 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 724006 707.037 0.690 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 735624 718.383 0.702 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 789622 771.115 0.753 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 797726 779.029 0.761 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 148 1103 1131 772 942 448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 821922 802.658 0.784 patch_______> segment topology patched using RTF: 75 ; ILE ; NTER segments residues atoms bonds angles dihedrals impropers: 2 148 1103 1131 1539 1879 448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 849522 829.611 0.810 patch_______> segment topology patched using RTF: 148 ; GLY ; CTER segments residues atoms bonds angles dihedrals impropers: 2 148 1104 1132 1541 1880 449 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 148 1104 1132 1541 1880 449 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 861042 840.861 0.821 patch_______> segment topology patched using RTF: 3 23 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 2 148 1104 1133 1543 1883 449 patch_______> segment topology patched using RTF: 16 44 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 2 148 1104 1134 1545 1886 449 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 861290 841.104 0.821 patch_______> segment topology patched using RTF: 29 33 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 2 148 1104 1135 1547 1889 449 patch_______> segment topology patched using RTF: 48 59 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 2 148 1104 1136 1549 1892 449 patch_______> segment topology patched using RTF: 60 65 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 2 148 1104 1137 1551 1895 449 patch_______> segment topology patched using RTF: 77 97 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 2 148 1104 1138 1553 1898 449 patch_______> segment topology patched using RTF: 90 118 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 2 148 1104 1139 1555 1901 449 patch_______> segment topology patched using RTF: 103 107 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 2 148 1104 1140 1557 1904 449 patch_______> segment topology patched using RTF: 122 133 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 2 148 1104 1141 1559 1907 449 patch_______> segment topology patched using RTF: 134 139 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 2 148 1104 1142 1561 1910 449 patch_s_522_> Number of disulfides patched in MODEL: 10 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 1 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 1072 32 openf___224_> Open 1hc9.ini wrpdb___568_> Residues, atoms, selected atoms: 148 1104 1104 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 968319 945.624 0.923 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 976511 953.624 0.931 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 992895 969.624 0.947 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1025663 1001.624 0.978 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1058431 1033.624 1.009 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1123967 1097.624 1.072 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1156735 1129.624 1.103 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1189503 1161.624 1.134 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1255039 1225.624 1.197 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1386111 1353.624 1.322 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 1142 1561 1902 433 Total number of restraints before, now : 0 5038 make_re_422_> Number of previous, current restraints : 0 5038 make_re_423_> Number of previous, current selected restraints: 0 5038 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1468834 1434.408 1.401 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 2abx getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1534386 1498.424 1.463 make_re_422_> Number of previous, current restraints : 5038 5182 make_re_423_> Number of previous, current selected restraints: 5038 5182 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1534386 1498.424 1.463 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 2abx getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 162 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 5182 5328 make_re_423_> Number of previous, current selected restraints: 5182 5166 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1534386 1498.424 1.463 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 2abx getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1599922 1562.424 1.526 make_re_422_> Number of previous, current restraints : 5328 5459 make_re_423_> Number of previous, current selected restraints: 5166 5297 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1599922 1562.424 1.526 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 2abx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 5459 5533 make_re_423_> Number of previous, current selected restraints: 5297 5371 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1599922 1562.424 1.526 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 2abx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 5533 5579 make_re_423_> Number of previous, current selected restraints: 5371 5417 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1599922 1562.424 1.526 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi4.mdt mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 2abx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 5579 5597 make_re_423_> Number of previous, current selected restraints: 5417 5435 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1917838 1872.889 1.829 make_re_422_> Number of previous, current restraints : 5597 8049 make_re_423_> Number of previous, current selected restraints: 5435 7887 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2048910 2000.889 1.954 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2179982 2128.889 2.079 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2442126 2384.889 2.329 make_re_422_> Number of previous, current restraints : 8049 10797 make_re_423_> Number of previous, current selected restraints: 7887 10635 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2573198 2512.889 2.454 make_re_422_> Number of previous, current restraints : 10797 13009 make_re_423_> Number of previous, current selected restraints: 10635 12847 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 13009 13662 make_re_423_> Number of previous, current selected restraints: 12847 13500 0 atoms in HETATM/BLK residues constrained to protein atoms within 2.30 angstroms and protein CA atoms within 10.00 angstroms make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 13662 13662 make_re_423_> Number of previous, current selected restraints: 13500 13500 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 13662 13662 make_re_423_> Number of previous, current selected restraints: 13500 13500 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 13662 13662 make_re_423_> Number of previous, current selected restraints: 13500 13500 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 13662 13662 make_re_423_> Number of previous, current selected restraints: 13500 13500 0 atoms in residues without defined topology constrained to be rigid bodies make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 13662 13662 make_re_423_> Number of previous, current selected restraints: 13500 13500 Dynamically allocated memory at amaxsymmetry [B,KiB,MiB]: 2574314 2513.979 2.455 define__645W> New number of symmetry segments, atom pairs: 1 74 rmdupl__427_> 949 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 13662 12551 openf___224_> Open 1hc9.rsr openf___224_> Open 1hc9.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2595612 2534.777 2.475 Dynamically allocated memory at amaxsymmetry [B,KiB,MiB]: 2596260 2535.410 2.476 rdcsr2__307_> Number of restraints read : 12551 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 12551 12551 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 openf___224_> Open 1hc9.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2596280 2535.430 2.476 read_mo_297_> Segments, residues, atoms: 2 148 1104 read_mo_298_> Segment: 1 1 A 74 A 553 read_mo_298_> Segment: 2 75 B 148 B 551 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1104 1104 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1104 7197 pick_re_612_> Number of MODEL atoms, selected restraints; 1104 7904 pick_re_612_> Number of MODEL atoms, selected restraints; 1104 8265 pick_re_612_> Number of MODEL atoms, selected restraints; 1104 8698 pick_re_612_> Number of MODEL atoms, selected restraints; 1104 9487 pick_re_612_> Number of MODEL atoms, selected restraints; 1104 10465 pick_re_612_> Number of MODEL atoms, selected restraints; 1104 11605 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2915360 2847.031 2.780 pick_re_612_> Number of MODEL atoms, selected restraints; 1104 12404 pick_re_612_> Number of MODEL atoms, selected restraints; 1104 12549 pick_re_612_> Number of MODEL atoms, selected restraints; 1104 12551 iupac_m_483_> CD1/2 CE1/2 swapped: 91.3623 24 24 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_487_> NH1/2 swapped: 178.8487 25 25 iupac_m_486_> OE1/2 will be swapped: -170.5022 41 41 iupac_m_486_> OE1/2 will be swapped: -170.3916 55 55 iupac_m_486_> OE1/2 will be swapped: 164.7045 56 56 iupac_m_487_> NH1/2 swapped: 179.1602 110 110 iupac_m_483_> CD1/2 CE1/2 swapped: -90.8184 128 128 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: -176.4305 130 130 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 148 Number of all, selected real atoms : 1104 1104 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 12551 12551 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1759 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 3111.9214 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 1132 0 0 0.008 0.008 22.177 1.000 2 Bond angle potential : 1541 4 22 3.314 3.314 327.08 1.000 3 Stereochemical cosine torsion poten: 781 0 90 61.152 61.152 423.37 1.000 4 Stereochemical improper torsion pot: 433 0 1 2.035 2.035 45.142 1.000 5 Soft-sphere overlap restraints : 1759 0 0 0.008 0.008 13.591 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 2452 9 12 0.431 0.431 432.53 1.000 10 Distance restraints 2 (N-O) : 2748 3 18 0.397 0.397 444.81 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 146 3 12 7.720 7.720 102.61 1.000 14 Sidechain Chi_1 dihedral restraints: 131 0 3 72.256 72.256 57.614 1.000 15 Sidechain Chi_2 dihedral restraints: 74 0 0 68.455 68.455 24.601 1.000 16 Sidechain Chi_3 dihedral restraints: 46 0 0 65.711 65.711 26.129 1.000 17 Sidechain Chi_4 dihedral restraints: 18 0 0 86.848 86.848 12.282 1.000 18 Disulfide distance restraints : 10 0 0 0.012 0.012 0.23544 1.000 19 Disulfide angle restraints : 20 0 0 2.796 2.796 3.4533 1.000 20 Disulfide dihedral angle restraints: 10 0 0 29.651 29.651 8.0825 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 2212 0 0 0.576 0.576 135.38 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 144 43 88 71.511 101.476 702.18 1.000 26 Distance restraints 4 (SDCH-SDCH) : 653 0 3 1.117 1.117 116.57 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 214.09 1.000 openf___224_> Open 1hc9.V99990001 # Heavy relative violation of each residue is written to: 1hc9.V99990001 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 25248.3301 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1682 53P 53P N CA 382 383 131.12 108.20 22.92 5.21 108.20 22.92 5.21 2 1823 66N 66N N CA 481 482 124.51 107.00 17.51 5.04 107.00 17.51 5.04 3 2450 126K 126K N CA 924 925 124.03 107.00 17.03 4.90 107.00 17.03 4.90 4 2461 127P 127P N CA 933 934 130.15 108.20 21.95 4.99 108.20 21.95 4.99 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 4136 65C 65C CA C 476 479 -156.94 -180.00 23.06 4.61 -180.00 23.06 4.61 2 4196 126K 126K CA C 925 931 -153.30 -180.00 26.70 5.34 -180.00 26.70 5.34 ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 3928 1I 2V C N 7 9 -88.94 -62.40 56.96 8.83 -62.40 56.96 8.83 1 2V 2V N CA 9 10 -92.79 -42.40 -42.40 2 3933 6T 7A C N 44 46 130.11 55.40 100.78 11.51 55.40 100.78 11.51 2 7A 7A N CA 46 47 105.83 38.20 38.20 3 3935 8T 9S C N 56 58 87.99 -136.60 146.96 4.62 -64.10 -168.29 17.31 3 9S 9S N CA 58 59 -151.70 151.20 -35.00 4 3936 9S 10P C N 62 64 -50.18 -64.50 38.25 2.27 -58.70 142.48 12.47 4 10P 10P N CA 64 65 111.73 147.20 -30.50 5 3938 11I 12S C N 77 79 -140.75 -64.10 101.77 8.72 -64.10 101.77 8.72 5 12S 12S N CA 79 80 31.94 -35.00 -35.00 6 3940 13A 14V C N 88 90 -39.55 -62.40 23.31 3.88 -125.40 -161.58 11.31 6 14V 14V N CA 90 91 -37.81 -42.40 143.30 7 3946 19G 20E C N 126 128 177.21 -117.80 77.04 3.85 54.60 133.59 17.44 7 20E 20E N CA 128 129 95.42 136.80 42.40 8 3947 20E 21N C N 135 137 133.88 -119.90 107.04 4.11 -63.20 -125.47 37.80 8 21N 21N N CA 137 138 150.19 137.00 -41.10 9 3948 21N 22L C N 143 145 75.84 60.20 121.44 8.59 -108.50 176.53 8.21 9 22L 22L N CA 145 146 150.02 29.60 132.50 10 3954 27M 28W C N 197 199 -175.77 -63.00 116.22 20.33 58.80 163.77 7.48 10 28W 28W N CA 199 200 -72.30 -44.20 33.00 11 3956 29C 30D C N 217 219 77.90 54.50 80.25 4.27 -70.90 -131.17 18.10 11 30D 30D N CA 219 220 -35.86 40.90 150.30 12 3957 30D 31V C N 225 227 91.25 55.90 52.97 2.98 -125.40 -157.34 11.50 12 31V 31V N CA 227 228 0.05 39.50 143.30 13 3961 34S 35S C N 255 257 -150.25 -136.60 22.18 0.77 -64.10 178.49 19.13 13 35S 35S N CA 257 258 168.68 151.20 -35.00 14 3968 41E 42L C N 308 310 -179.51 -108.50 87.55 4.81 60.20 130.93 15.87 14 42L 42L N CA 310 311 81.29 132.50 29.60 15 3969 42L 43G C N 316 318 -159.07 -62.40 103.67 19.54 -62.40 103.67 19.54 15 43G 43G N CA 318 319 -78.66 -41.20 -41.20 16 3971 44C 45A C N 326 328 176.56 -134.00 94.30 5.78 55.40 124.47 14.51 16 45A 45A N CA 328 329 66.70 147.00 38.20 17 3972 45A 46A C N 331 333 110.99 -134.00 132.78 3.09 -62.50 -156.82 33.45 17 46A 46A N CA 333 334 -146.65 147.00 -40.90 18 3974 47T 48C C N 343 345 -25.88 -69.10 70.48 3.82 57.40 97.20 7.84 18 48C 48C N CA 345 346 86.12 141.80 36.00 19 3981 54Y 55E C N 399 401 -16.67 -69.30 101.51 9.18 -69.30 101.51 9.18 19 55E 55E N CA 401 402 -130.70 142.50 142.50 20 3989 62T 63D C N 456 458 -171.66 -63.30 121.65 20.77 54.50 -169.04 11.55 20 63D 63D N CA 458 459 -95.30 -40.00 40.90 21 3991 64K 65C C N 473 475 -166.76 -63.00 106.57 18.72 57.40 169.55 12.06 21 65C 65C N CA 475 476 -65.45 -41.10 36.00 22 4005 80T 81A C N 597 599 172.22 -134.00 86.14 5.18 55.40 123.97 14.68 22 81A 81A N CA 599 600 79.71 147.00 38.20 23 4006 81A 82T C N 602 604 108.25 55.90 123.37 12.51 -124.80 127.18 6.54 23 82T 82T N CA 604 605 151.22 39.50 143.50 24 4012 87A 88V C N 641 643 66.65 55.90 79.59 4.80 -125.40 -115.75 6.95 24 88V 88V N CA 643 644 -39.36 39.50 143.30 25 4014 89T 90C C N 655 657 57.00 -69.10 132.56 12.27 -117.90 179.77 6.85 25 90C 90C N CA 657 658 -177.31 141.80 141.10 26 4018 93G 94E C N 679 681 -178.36 -117.80 60.93 2.40 -63.60 -154.60 23.75 26 94E 94E N CA 681 682 130.05 136.80 -40.30 27 4019 94E 95N C N 688 690 83.81 55.90 111.54 9.91 -63.20 -134.18 24.73 27 95N 95N N CA 690 691 147.49 39.50 -41.10 28 4020 95N 96L C N 696 698 56.16 60.20 107.71 6.07 -108.50 164.73 7.90 28 96L 96L N CA 698 699 137.24 29.60 132.50 29 4025 100K 101M C N 742 744 91.25 56.30 79.13 10.43 -125.60 147.30 6.68 29 101M 101M N CA 744 745 105.80 34.80 140.50 30 4026 101M 102W C N 750 752 -102.03 -63.00 40.40 7.08 -63.00 40.40 7.08 30 102W 102W N CA 752 753 -54.66 -44.20 -44.20 31 4032 107C 108S C N 800 802 -166.28 -136.60 93.03 5.18 -64.10 141.60 11.67 31 108S 108S N CA 802 803 63.03 151.20 -35.00 32 4033 108S 109S C N 806 808 176.91 -136.60 86.79 3.19 56.90 -150.35 9.82 32 109S 109S N CA 808 809 -135.51 151.20 36.40 33 4035 110R 111G C N 823 825 -60.51 -62.40 41.17 6.24 82.20 142.97 9.89 33 111G 111G N CA 825 826 -0.08 -41.20 8.50 34 4044 119A 120A C N 882 884 92.41 -134.00 136.78 3.54 -62.50 -149.36 32.86 34 120A 120A N CA 884 885 176.37 147.00 -40.90 35 4046 121T 122C C N 894 896 -24.43 -69.10 73.82 3.98 57.40 94.38 7.79 35 122C 122C N CA 896 897 83.03 141.80 36.00 36 4048 123P 124S C N 907 909 109.55 -136.60 151.31 4.75 -64.10 -171.18 20.35 36 124S 124S N CA 909 910 -109.13 151.20 -35.00 37 4050 125K 126K C N 922 924 -108.16 -62.90 55.71 9.68 -62.90 55.71 9.68 37 126K 126K N CA 924 925 -73.28 -40.80 -40.80 38 4052 127P 128Y C N 938 940 -112.49 -124.30 81.49 4.83 -98.40 88.76 9.40 38 128Y 128Y N CA 940 941 -143.97 135.40 128.40 39 4059 134C 135S C N 994 996 138.31 56.90 81.44 9.68 56.90 81.44 9.68 39 135S 135S N CA 996 997 38.69 36.40 36.40 40 4061 136T 137D C N 1007 1009 172.17 -63.30 130.22 21.98 -96.50 -169.00 8.04 40 137D 137D N CA 1009 1010 -78.05 -40.00 114.20 41 4063 138K 139C C N 1024 1026 -178.67 -63.00 121.94 21.65 57.40 169.56 10.23 41 139C 139C N CA 1026 1027 -79.72 -41.10 36.00 42 4064 139C 140N C N 1030 1032 -102.69 -119.90 87.20 3.54 -63.20 100.68 10.95 42 140N 140N N CA 1032 1033 51.51 137.00 -41.10 43 4069 144K 145Q C N 1071 1073 -135.92 -121.10 98.95 4.44 -73.00 115.48 6.64 43 145Q 145Q N CA 1073 1074 -122.47 139.70 140.70 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 1 15 22 100 59 93 95 96 123 113 136 << end of ENERGY. report__> Symmetry breaking contribution to -Ln[Molec.pdf]: All Diff larger than cutoff are reported: 1.00000 Atm1A Atm2A Atm1B Atm2B WghA WghB DistA DistB Diff Term ------------------------------------------------------------------------ 59 383 612 934 1.000 1.000 22.916 21.874 1.042 1.086 98 146 651 699 1.000 1.000 9.203 10.210 -1.007 1.013 383 411 934 962 1.000 1.000 8.199 9.458 -1.260 1.587 383 420 934 971 1.000 1.000 8.322 9.527 -1.205 1.453 383 427 934 978 1.000 1.000 11.300 12.647 -1.347 1.814 openf___224_> Open 1hc9.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 148 1104 1104 >> Summary of successfully produced models: Filename molpdf ---------------------------------------- 1hc9.B99990001.pdb 3111.92139 Dynamically allocated memory at finish [B,KiB,MiB]: 2915360 2847.031 2.780 Starting time : 2016/04/05 22:41:21 Closing time : 2016/04/05 22:41:30 Total CPU time [seconds] : 8.12