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): 2019/05/05 16:19:19 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 bak_star4.pir 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]: 272829 266.435 0.260 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 333713 325.892 0.318 check_prot_W> Alignment sequence domain0 protein type '' does not contain 'sequence' or 'structure'; it will be treated as a sequence without structure Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 334361 326.524 0.319 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 334937 327.087 0.319 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 335517 327.653 0.320 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 335877 328.005 0.320 Read the alignment from file : bak_star4.pir Total number of alignment positions: 163 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5XYIH 163 1 5XYIH 2 5XXUH 145 1 5XXUH 3 3J60H 146 1 3J60H 4 domain0 91 1 check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ./5XYIH.atm Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 386502 377.443 0.369 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 386502 377.443 0.369 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 386673 377.610 0.369 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 387523 378.440 0.370 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 388781 379.669 0.371 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 390685 381.528 0.373 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 390685 381.528 0.373 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 390775 381.616 0.373 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 393631 384.405 0.375 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 393631 384.405 0.375 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 393766 384.537 0.376 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 398050 388.721 0.380 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 398050 388.721 0.380 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 398248 388.914 0.380 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 404674 395.189 0.386 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 404674 395.189 0.386 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 404971 395.479 0.386 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 414593 404.876 0.395 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 414593 404.876 0.395 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 415043 405.315 0.396 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 429493 419.427 0.410 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 429493 419.427 0.410 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 430168 420.086 0.410 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 451826 441.236 0.431 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 451268 440.691 0.430 openf___224_> Open ./5XXUH.atm Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 496493 484.856 0.473 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 496493 484.856 0.473 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 496664 485.023 0.474 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 497514 485.854 0.474 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 498772 487.082 0.476 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 500676 488.941 0.477 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 500676 488.941 0.477 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 500766 489.029 0.478 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 503622 491.818 0.480 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 503622 491.818 0.480 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 503757 491.950 0.480 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 508041 496.134 0.485 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 508041 496.134 0.485 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 508239 496.327 0.485 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 514665 502.603 0.491 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 514665 502.603 0.491 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 514962 502.893 0.491 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 524584 512.289 0.500 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 524584 512.289 0.500 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 525034 512.729 0.501 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 539484 526.840 0.514 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 539439 526.796 0.514 openf___224_> Open ./3J60H.atm Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 584964 571.254 0.558 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 584964 571.254 0.558 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 585135 571.421 0.558 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 585985 572.251 0.559 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 587243 573.479 0.560 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 589147 575.339 0.562 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 589147 575.339 0.562 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 589237 575.427 0.562 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 592093 578.216 0.565 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 592093 578.216 0.565 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 592228 578.348 0.565 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 596512 582.531 0.569 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 596512 582.531 0.569 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 596710 582.725 0.569 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 603136 589.000 0.575 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 603136 589.000 0.575 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 603433 589.290 0.575 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 613055 598.687 0.585 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 613055 598.687 0.585 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 613505 599.126 0.585 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 627955 613.237 0.599 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 627919 613.202 0.599 check_ali___> Checking pairwise structural superpositions. Equivalent CA pairs with distance difference larger than 6.0 angstroms: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- END OF TABLE 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 ---------------------------------------------- 76 1 76 146 V A 24.900 76 2 70 128 V A 24.219 76 3 71 129 V A 24.598 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]: 767171 749.190 0.732 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 768771 750.753 0.733 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 772751 754.640 0.737 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 774751 756.593 0.739 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 777751 759.522 0.742 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 782251 763.917 0.746 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 787823 769.358 0.751 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 790623 772.093 0.754 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 794823 776.194 0.758 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 801123 782.347 0.764 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 803895 785.054 0.767 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 805295 786.421 0.768 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 819425 800.220 0.781 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 886849 866.063 0.846 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 896569 875.556 0.855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 91 669 679 0 0 268 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 925049 903.368 0.882 patch_______> segment topology patched using RTF: 1 ; THR ; NTER segments residues atoms bonds angles dihedrals impropers: 1 91 669 679 921 1091 268 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 955985 933.579 0.912 patch_______> segment topology patched using RTF: 91 ; THR ; CTER segments residues atoms bonds angles dihedrals impropers: 1 91 670 680 923 1093 269 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 91 670 680 923 1093 269 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 3 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 540 130 openf___224_> Open domain0.ini wrpdb___568_> Residues, atoms, selected atoms: 91 670 670 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1063014 1038.100 1.014 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1071206 1046.100 1.022 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1087590 1062.100 1.037 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1120358 1094.100 1.068 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1153126 1126.100 1.100 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1218662 1190.100 1.162 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1251430 1222.100 1.193 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 680 923 1044 264 Total number of restraints before, now : 0 2911 make_re_422_> Number of previous, current restraints : 0 2911 make_re_423_> Number of previous, current selected restraints: 0 2911 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1301784 1271.273 1.241 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 1 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 2 ASN errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 3 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 4 VAL errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 6 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 7 CYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 8 LEU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 9 PHE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 10 ASP errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 11 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 12 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 13 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 45 GLN errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 46 THR errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 1 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 2 ASN errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 3 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 6 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 8 LEU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 9 PHE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 10 ASP errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 11 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 12 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 13 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 45 GLN errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 3 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 6 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 12 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 13 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 45 GLN errdih__638_> Missing atoms in a dihedral, residue index, residue type: 8 6 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 8 13 LYS getdata_643_> Protein accepted: 5XYIH getdata_643_> Protein accepted: 5XXUH getdata_643_> Protein accepted: 3J60H getdata_289_> Proteins (all/accepted): 3 3 make_re_422_> Number of previous, current restraints : 2911 3000 make_re_423_> Number of previous, current selected restraints: 2911 3000 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1301848 1271.336 1.242 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 5XYIH getdata_643_> Protein accepted: 5XXUH getdata_643_> Protein accepted: 3J60H getdata_289_> Proteins (all/accepted): 3 3 omgdel__425_> Unselected all O C +N +CA dihedrals: 95 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 3000 3090 make_re_423_> Number of previous, current selected restraints: 3000 2995 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1301848 1271.336 1.242 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 5XYIH getdata_643_> Protein accepted: 5XXUH getdata_643_> Protein accepted: 3J60H getdata_289_> Proteins (all/accepted): 3 3 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1334616 1303.336 1.273 make_re_422_> Number of previous, current restraints : 3090 3166 make_re_423_> Number of previous, current selected restraints: 2995 3071 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1334616 1303.336 1.273 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 5XYIH getdata_643_> Protein accepted: 5XXUH getdata_643_> Protein accepted: 3J60H getdata_289_> Proteins (all/accepted): 3 3 make_re_422_> Number of previous, current restraints : 3166 3214 make_re_423_> Number of previous, current selected restraints: 3071 3119 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1334616 1303.336 1.273 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 5XYIH getdata_643_> Protein accepted: 5XXUH getdata_643_> Protein accepted: 3J60H getdata_289_> Proteins (all/accepted): 3 3 make_re_422_> Number of previous, current restraints : 3214 3236 make_re_423_> Number of previous, current selected restraints: 3119 3141 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1334616 1303.336 1.273 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: 5XYIH getdata_643_> Protein accepted: 5XXUH getdata_643_> Protein accepted: 3J60H getdata_289_> Proteins (all/accepted): 3 3 make_re_422_> Number of previous, current restraints : 3236 3244 make_re_423_> Number of previous, current selected restraints: 3141 3149 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1527540 1491.738 1.457 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1593076 1555.738 1.519 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1724148 1683.738 1.644 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1789684 1747.738 1.707 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2051828 2003.738 1.957 make_re_422_> Number of previous, current restraints : 3244 4636 make_re_423_> Number of previous, current selected restraints: 3149 4541 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2182900 2131.738 2.082 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2248436 2195.738 2.144 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2772724 2707.738 2.644 make_re_422_> Number of previous, current restraints : 4636 6197 make_re_423_> Number of previous, current selected restraints: 4541 6102 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 6197 7016 make_re_423_> Number of previous, current selected restraints: 6102 6921 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 7016 7111 make_re_423_> Number of previous, current selected restraints: 6921 7016 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 : 7111 7111 make_re_423_> Number of previous, current selected restraints: 7016 7016 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 7111 7111 make_re_423_> Number of previous, current selected restraints: 7016 7016 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 7111 7111 make_re_423_> Number of previous, current selected restraints: 7016 7016 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 7111 7111 make_re_423_> Number of previous, current selected restraints: 7016 7016 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 : 7111 7111 make_re_423_> Number of previous, current selected restraints: 7016 7016 rmdupl__427_> 539 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 7111 6477 openf___224_> Open domain0.rsr openf___224_> Open domain0.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2488355 2430.034 2.373 rdcsr2__307_> Number of restraints read : 6477 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 6477 6477 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 openf___224_> Open domain0.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2488375 2430.054 2.373 read_mo_297_> Segments, residues, atoms: 1 91 670 read_mo_298_> Segment: 1 1 91 670 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 670 670 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 670 3713 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4176 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4448 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4819 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5209 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5609 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2797039 2731.483 2.667 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6255 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6477 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6477 iupac_m_487_> NH1/2 swapped: 179.6756 16 16 iupac_m_486_> OE1/2 will be swapped: -94.0911 20 20 iupac_m_487_> NH1/2 swapped: 179.7331 21 21 iupac_m_487_> NH1/2 swapped: 175.6288 26 26 iupac_m_486_> OE1/2 will be swapped: -163.0793 46 46 iupac_m_485_> OD1/2 will be swapped: -166.7937 47 47 iupac_m_485_> OD1/2 will be swapped: 179.3877 59 59 iupac_m_486_> OE1/2 will be swapped: -175.8256 65 65 iupac_m_485_> OD1/2 will be swapped: -166.2317 73 73 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 91 Number of all, selected real atoms : 670 670 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 6477 6477 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1315 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 : 3365.3289 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 : 680 0 0 0.005 0.005 4.1361 1.000 2 Bond angle potential : 923 0 0 1.870 1.870 58.165 1.000 3 Stereochemical cosine torsion poten: 410 0 18 52.807 52.807 171.45 1.000 4 Stereochemical improper torsion pot: 264 0 0 1.157 1.157 6.9768 1.000 5 Soft-sphere overlap restraints : 1315 0 0 0.003 0.003 1.5169 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) : 1392 6 11 0.704 0.704 1004.5 1.000 10 Distance restraints 2 (N-O) : 1561 6 24 0.844 0.844 1170.6 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: 90 0 0 3.542 3.542 13.313 1.000 14 Sidechain Chi_1 dihedral restraints: 76 0 1 88.752 88.752 25.740 1.000 15 Sidechain Chi_2 dihedral restraints: 48 0 0 72.885 72.885 24.267 1.000 16 Sidechain Chi_3 dihedral restraints: 22 0 0 67.648 67.648 14.428 1.000 17 Sidechain Chi_4 dihedral restraints: 8 0 0 100.115 100.115 4.1829 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 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) : 819 0 0 0.559 0.559 715.66 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: 89 17 12 33.708 75.185 60.412 1.000 26 Distance restraints 4 (SDCH-SDCH) : 95 0 2 1.737 1.737 89.994 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 0.0000 1.000 openf___224_> Open domain0.V99990001 # Heavy relative violation of each residue is written to: domain0.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: 11394.9834 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 9 : Distance restraints 1 (CA-CA) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 3333 31S 77A CA CA 228 564 10.53 5.57 4.96 10.71 5.57 4.96 10.71 2 3354 32T 77A CA CA 234 564 13.37 7.99 5.37 5.72 7.99 5.37 5.72 3 3369 33H 77A CA CA 241 564 14.38 8.47 5.91 5.89 8.47 5.91 5.89 4 3387 34A 77A CA CA 251 564 13.99 9.00 4.99 4.95 9.00 4.99 4.95 5 3405 35L 77A CA CA 256 564 12.11 7.71 4.40 4.61 7.71 4.40 4.61 6 3429 36A 77A CA CA 264 564 8.94 6.12 2.82 4.90 6.12 2.82 4.90 ------------------------------------------------------------------------------------------------- Feature 10 : Distance restraints 2 (N-O) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 4517 31S 77A N O 227 567 11.24 6.73 4.51 4.74 6.73 4.51 4.74 2 5053 61A 57P N O 440 414 5.58 2.81 2.77 5.07 2.81 2.77 5.07 3 5324 77A 31S N O 563 232 14.27 5.38 8.89 14.41 5.38 8.89 14.41 4 5325 77A 32T N O 563 239 16.34 9.74 6.59 6.02 9.74 6.59 6.02 5 5326 77A 33H N O 563 249 13.72 6.50 7.22 8.04 6.50 7.22 8.04 6 5327 77A 34A N O 563 254 13.47 8.23 5.24 5.57 8.23 5.24 5.57 ------------------------------------------------------------------------------------------------- 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 2278 1T 2R C N 6 8 -65.06 -63.00 15.89 2.02 -125.20 176.50 7.02 1 2R 2R N CA 8 9 -25.34 -41.10 140.60 2 2288 11S 12N C N 72 74 -80.46 -71.20 69.10 4.69 -63.20 116.71 13.71 2 12N 12N N CA 74 75 74.32 142.80 -41.10 3 2290 13C 14H C N 86 88 -96.22 -125.60 70.28 2.06 -63.20 121.81 13.50 3 14H 14H N CA 88 89 74.95 138.80 -42.30 4 2300 23E 24D C N 167 169 -97.79 -63.30 76.14 11.62 -63.30 76.14 11.62 4 24D 24D N CA 169 170 -107.88 -40.00 -40.00 5 2307 30N 31S C N 225 227 -91.33 -72.40 36.34 1.66 -64.10 144.17 12.27 5 31S 31S N CA 227 228 -176.58 152.40 -35.00 6 2308 31S 32T C N 231 233 -62.21 -63.20 12.17 1.50 -124.80 173.93 9.24 6 32T 32T N CA 233 234 -54.23 -42.10 143.50 7 2318 41I 42R C N 300 302 -62.96 -72.10 10.36 0.88 -63.00 172.13 23.25 7 42R 42R N CA 302 303 146.78 141.90 -41.10 8 2323 46E 47D C N 338 340 -66.16 -70.90 4.85 0.39 -63.30 168.68 20.99 8 47D 47D N CA 340 341 151.35 150.30 -40.00 9 2324 47D 48N C N 346 348 79.48 55.90 79.37 4.07 -63.20 142.76 21.84 9 48N 48N N CA 348 349 -36.28 39.50 -41.10 10 2327 50N 51A C N 367 369 -65.15 -68.20 13.52 0.98 -62.50 173.04 28.23 10 51A 51A N CA 369 370 132.13 145.30 -40.90 11 2328 51A 52G C N 372 374 71.35 78.70 42.83 0.92 -80.20 163.74 12.06 11 52G 52G N CA 374 375 -123.91 -166.10 174.10 12 2333 56A 57P C N 406 408 -65.34 -64.50 15.81 1.14 -58.70 166.65 14.31 12 57P 57P N CA 408 409 162.99 147.20 -30.50 13 2334 57P 58S C N 413 415 78.00 56.90 76.47 3.37 -64.10 142.12 18.15 13 58S 58S N CA 415 416 -37.10 36.40 -35.00 14 2341 64P 65E C N 468 470 58.72 54.60 5.39 0.69 -63.60 149.63 25.72 14 65E 65E N CA 470 471 45.87 42.40 -40.30 15 2351 74L 75Q C N 545 547 -134.14 -121.10 22.51 0.79 -63.80 176.29 29.62 15 75Q 75Q N CA 547 548 158.04 139.70 -40.30 16 2353 76V 77A C N 561 563 154.69 -134.00 74.25 1.80 -62.50 -151.88 41.41 16 77A 77A N CA 563 564 167.71 147.00 -40.90 17 2354 77A 78M C N 566 568 -84.63 -73.00 42.58 2.71 -63.40 137.19 22.17 17 78M 78M N CA 568 569 -176.04 143.00 -40.50 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 0 9 18 42 54 63 92 59 104 100 95 << end of ENERGY. openf___224_> Open domain0.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 91 670 670 openf___224_> Open domain0.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2797059 2731.503 2.667 read_mo_297_> Segments, residues, atoms: 1 91 670 read_mo_298_> Segment: 1 1 91 670 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 670 670 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 670 3713 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4176 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4448 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4819 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5209 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5609 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6255 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6477 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6477 iupac_m_486_> OE1/2 will be swapped: 177.5203 20 20 iupac_m_487_> NH1/2 swapped: 179.3054 26 26 iupac_m_486_> OE1/2 will be swapped: -179.7771 28 28 iupac_m_487_> NH1/2 swapped: 179.6666 42 42 iupac_m_486_> OE1/2 will be swapped: 108.7800 65 65 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 91 Number of all, selected real atoms : 670 670 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 6477 6477 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1333 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 : 3689.8535 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 : 680 0 1 0.008 0.008 11.239 1.000 2 Bond angle potential : 923 7 9 5.708 5.708 393.39 1.000 3 Stereochemical cosine torsion poten: 410 0 15 50.346 50.346 158.29 1.000 4 Stereochemical improper torsion pot: 264 0 0 1.069 1.069 5.9070 1.000 5 Soft-sphere overlap restraints : 1333 1 1 0.009 0.009 11.569 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) : 1392 3 14 0.716 0.716 1002.0 1.000 10 Distance restraints 2 (N-O) : 1561 3 25 0.824 0.824 1166.5 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: 90 0 0 4.342 4.342 20.013 1.000 14 Sidechain Chi_1 dihedral restraints: 76 0 1 84.533 84.533 23.193 1.000 15 Sidechain Chi_2 dihedral restraints: 48 0 0 77.710 77.710 22.111 1.000 16 Sidechain Chi_3 dihedral restraints: 22 0 0 61.525 61.525 11.053 1.000 17 Sidechain Chi_4 dihedral restraints: 8 0 0 108.725 108.725 6.3001 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 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) : 819 0 0 0.556 0.556 715.30 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: 89 17 12 35.144 74.801 56.663 1.000 26 Distance restraints 4 (SDCH-SDCH) : 95 0 1 1.425 1.425 86.293 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 0.0000 1.000 openf___224_> Open domain0.V99990002 # Heavy relative violation of each residue is written to: domain0.V99990002 # 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: 11188.8379 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 1302 62F 62F CB CG 447 448 153.54 122.30 31.25 6.79 122.30 31.25 6.79 ------------------------------------------------------------------------------------------------- Feature 9 : Distance restraints 1 (CA-CA) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 3333 31S 77A CA CA 228 564 10.31 5.57 4.75 10.24 5.57 4.75 10.24 2 3354 32T 77A CA CA 234 564 12.32 7.99 4.32 4.60 7.99 4.32 4.60 3 3369 33H 77A CA CA 241 564 14.85 8.47 6.37 6.35 8.47 6.37 6.35 ------------------------------------------------------------------------------------------------- Feature 10 : Distance restraints 2 (N-O) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 4517 31S 77A N O 227 567 11.19 6.73 4.46 4.69 6.73 4.46 4.69 2 5324 77A 31S N O 563 232 13.39 5.38 8.01 12.98 5.38 8.01 12.98 3 5326 77A 33H N O 563 249 15.80 6.50 9.31 10.36 6.50 9.31 10.36 ------------------------------------------------------------------------------------------------- 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 2280 3C 4G C N 23 25 -78.99 -80.20 10.39 0.47 -62.40 135.40 21.06 1 4G 4G N CA 25 26 -175.58 174.10 -41.20 2 2281 4G 5C C N 27 29 75.28 -63.00 141.28 21.83 -63.00 141.28 21.83 2 5C 5C N CA 29 30 -70.05 -41.10 -41.10 3 2290 13C 14H C N 86 88 62.73 56.30 10.83 0.89 -63.20 146.26 25.12 3 14H 14H N CA 88 89 32.09 40.80 -42.30 4 2299 22I 23E C N 158 160 -73.64 -63.60 10.92 1.50 -117.80 178.37 8.02 4 23E 23E N CA 160 161 -36.02 -40.30 136.80 5 2300 23E 24D C N 167 169 63.14 -63.30 178.37 20.17 -63.30 178.37 20.17 5 24D 24D N CA 169 170 -165.81 -40.00 -40.00 6 2307 30N 31S C N 225 227 -136.65 -136.60 70.71 3.59 -64.10 126.06 14.37 6 31S 31S N CA 227 228 -138.09 151.20 -35.00 7 2309 32T 33H C N 238 240 -60.31 -63.20 13.25 1.50 -125.60 178.35 7.79 7 33H 33H N CA 240 241 -55.23 -42.30 138.80 8 2319 42R 43A C N 311 313 90.67 55.40 75.87 2.77 -62.50 153.63 30.00 8 43A 43A N CA 313 314 -28.98 38.20 -40.90 9 2327 50N 51A C N 367 369 -91.99 -68.20 34.48 3.40 -62.50 163.91 25.58 9 51A 51A N CA 369 370 120.34 145.30 -40.90 10 2328 51A 52G C N 372 374 86.21 82.20 11.06 0.72 -80.20 -132.38 7.61 10 52G 52G N CA 374 375 18.81 8.50 174.10 11 2329 52G 53N C N 376 378 -71.40 -63.20 14.11 1.52 55.90 144.86 17.87 11 53N 53N N CA 378 379 -29.62 -41.10 39.50 12 2340 63T 64P C N 461 463 -89.13 -64.50 28.34 2.17 -58.70 171.01 16.64 12 64P 64P N CA 463 464 161.22 147.20 -30.50 13 2341 64P 65E C N 468 470 -86.70 -69.30 42.19 3.73 -63.60 146.20 18.32 13 65E 65E N CA 470 471 104.06 142.50 -40.30 14 2349 72V 73D C N 529 531 -55.09 -63.30 8.22 1.28 -96.50 160.14 6.75 14 73D 73D N CA 531 532 -40.49 -40.00 114.20 15 2351 74L 75Q C N 545 547 179.76 -121.10 68.25 2.10 -63.80 -173.30 33.14 15 75Q 75Q N CA 547 548 173.77 139.70 -40.30 16 2353 76V 77A C N 561 563 -88.27 -68.20 60.90 4.22 -62.50 119.12 20.88 16 77A 77A N CA 563 564 -157.20 145.30 -40.90 17 2354 77A 78M C N 566 568 -53.13 -73.00 39.70 3.03 -63.40 142.50 20.50 17 78M 78M N CA 568 569 177.37 143.00 -40.50 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 0 12 16 46 50 59 70 70 89 97 116 << end of ENERGY. openf___224_> Open domain0.B99990002.pdb wrpdb___568_> Residues, atoms, selected atoms: 91 670 670 openf___224_> Open domain0.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2797059 2731.503 2.667 read_mo_297_> Segments, residues, atoms: 1 91 670 read_mo_298_> Segment: 1 1 91 670 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 670 670 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 670 3713 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4176 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4448 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4819 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5209 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5609 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6255 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6477 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6477 iupac_m_487_> NH1/2 swapped: 168.4640 2 2 iupac_m_486_> OE1/2 will be swapped: 102.6588 20 20 iupac_m_485_> OD1/2 will be swapped: 139.7895 24 24 iupac_m_487_> NH1/2 swapped: -178.8572 42 42 iupac_m_485_> OD1/2 will be swapped: 115.8747 47 47 iupac_m_483_> CD1/2 CE1/2 swapped: -98.1227 62 62 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: -146.5405 65 65 iupac_m_485_> OD1/2 will be swapped: 167.5125 73 73 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 91 Number of all, selected real atoms : 670 670 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 6477 6477 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1217 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 : 3420.8613 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 : 680 0 0 0.005 0.005 4.5089 1.000 2 Bond angle potential : 923 0 1 2.092 2.092 74.612 1.000 3 Stereochemical cosine torsion poten: 410 0 13 50.644 50.644 162.49 1.000 4 Stereochemical improper torsion pot: 264 0 0 1.139 1.139 6.6762 1.000 5 Soft-sphere overlap restraints : 1217 0 0 0.003 0.003 1.7379 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) : 1392 4 14 0.728 0.728 1004.6 1.000 10 Distance restraints 2 (N-O) : 1561 4 26 0.870 0.870 1190.8 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: 90 0 0 4.217 4.217 18.876 1.000 14 Sidechain Chi_1 dihedral restraints: 76 0 1 86.080 86.080 22.900 1.000 15 Sidechain Chi_2 dihedral restraints: 48 0 0 83.230 83.230 25.955 1.000 16 Sidechain Chi_3 dihedral restraints: 22 0 0 70.479 70.479 14.135 1.000 17 Sidechain Chi_4 dihedral restraints: 8 0 0 87.133 87.133 5.9798 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 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) : 819 0 0 0.561 0.561 713.01 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: 89 18 12 38.471 81.968 85.793 1.000 26 Distance restraints 4 (SDCH-SDCH) : 95 0 1 1.464 1.464 88.753 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 0.0000 1.000 openf___224_> Open domain0.V99990003 # Heavy relative violation of each residue is written to: domain0.V99990003 # 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: 11751.7617 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 9 : Distance restraints 1 (CA-CA) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 3333 31S 77A CA CA 228 564 10.72 5.57 5.16 11.13 5.57 5.16 11.13 2 3354 32T 77A CA CA 234 564 13.17 7.99 5.18 5.51 7.99 5.18 5.51 3 3369 33H 77A CA CA 241 564 14.69 8.47 6.22 6.20 8.47 6.22 6.20 4 3387 34A 77A CA CA 251 564 13.68 9.00 4.68 4.65 9.00 4.68 4.65 ------------------------------------------------------------------------------------------------- Feature 10 : Distance restraints 2 (N-O) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 4517 31S 77A N O 227 567 11.59 6.73 4.85 5.11 6.73 4.85 5.11 2 5324 77A 31S N O 563 232 14.26 5.38 8.88 14.39 5.38 8.88 14.39 3 5326 77A 33H N O 563 249 15.44 6.50 8.94 9.95 6.50 8.94 9.95 4 5327 77A 34A N O 563 254 12.88 8.23 4.65 4.95 8.23 4.65 4.95 ------------------------------------------------------------------------------------------------- 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 2288 11S 12N C N 72 74 -82.20 -63.20 80.42 9.14 -63.20 80.42 9.14 1 12N 12N N CA 74 75 37.04 -41.10 -41.10 2 2290 13C 14H C N 86 88 65.07 56.30 17.61 1.33 -63.20 145.10 24.92 2 14H 14H N CA 88 89 25.54 40.80 -42.30 3 2300 23E 24D C N 167 169 -95.42 -96.50 100.36 4.22 -63.30 110.23 15.68 3 24D 24D N CA 169 170 -145.45 114.20 -40.00 4 2307 30N 31S C N 225 227 -124.91 -136.60 21.66 1.23 -64.10 167.03 16.40 4 31S 31S N CA 227 228 169.43 151.20 -35.00 5 2318 41I 42R C N 300 302 -64.27 -72.10 10.25 0.89 -63.00 170.39 23.10 5 42R 42R N CA 302 303 148.52 141.90 -41.10 6 2322 45S 46E C N 329 331 -64.24 -69.30 18.63 1.58 -63.60 159.27 21.27 6 46E 46E N CA 331 332 160.43 142.50 -40.30 7 2323 46E 47D C N 338 340 75.63 54.50 67.17 3.50 -63.30 139.99 22.93 7 47D 47D N CA 340 341 -22.86 40.90 -40.00 8 2327 50N 51A C N 367 369 -92.62 -68.20 39.39 3.85 -62.50 158.19 24.62 8 51A 51A N CA 369 370 114.40 145.30 -40.90 9 2328 51A 52G C N 372 374 85.08 82.20 14.26 0.83 -80.20 -135.70 7.59 9 52G 52G N CA 374 375 22.47 8.50 174.10 10 2329 52G 53N C N 376 378 -68.50 -63.20 7.02 0.80 55.90 145.78 17.94 10 53N 53N N CA 378 379 -36.50 -41.10 39.50 11 2335 58S 59D C N 419 421 -77.48 -70.90 30.09 1.18 -63.30 141.05 18.30 11 59D 59D N CA 421 422 179.66 150.30 -40.00 12 2336 59D 60R C N 427 429 75.88 -63.00 141.71 21.90 -63.00 141.71 21.90 12 60R 60R N CA 429 430 -69.26 -41.10 -41.10 13 2340 63T 64P C N 461 463 -80.63 -64.50 16.57 1.52 -58.70 179.87 16.67 13 64P 64P N CA 463 464 150.97 147.20 -30.50 14 2341 64P 65E C N 468 470 -89.92 -117.80 52.01 1.92 -63.60 135.77 16.79 14 65E 65E N CA 470 471 92.89 136.80 -40.30 15 2346 69C 70M C N 504 506 -62.28 -63.40 4.48 0.59 -125.60 -174.22 9.90 15 70M 70M N CA 506 507 -44.84 -40.50 140.50 16 2351 74L 75Q C N 545 547 -148.74 -121.10 29.91 1.37 -63.80 -171.23 24.39 16 75Q 75Q N CA 547 548 128.28 139.70 -40.30 17 2353 76V 77A C N 561 563 155.28 -134.00 77.02 1.75 -62.50 -159.31 40.10 17 77A 77A N CA 563 564 177.51 147.00 -40.90 18 2354 77A 78M C N 566 568 -75.00 -73.00 44.72 2.99 -63.40 132.34 20.68 18 78M 78M N CA 568 569 -172.33 143.00 -40.50 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 0 11 4 27 54 70 70 59 95 97 81 << end of ENERGY. openf___224_> Open domain0.B99990003.pdb wrpdb___568_> Residues, atoms, selected atoms: 91 670 670 openf___224_> Open domain0.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2797059 2731.503 2.667 read_mo_297_> Segments, residues, atoms: 1 91 670 read_mo_298_> Segment: 1 1 91 670 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 670 670 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 670 3713 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4176 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4448 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4819 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5209 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5609 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6255 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6477 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6477 iupac_m_487_> NH1/2 swapped: -178.0363 21 21 iupac_m_486_> OE1/2 will be swapped: 122.4868 28 28 iupac_m_487_> NH1/2 swapped: 177.8858 60 60 iupac_m_483_> CD1/2 CE1/2 swapped: 105.4211 62 62 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: 178.0902 65 65 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 91 Number of all, selected real atoms : 670 670 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 6477 6477 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1305 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 : 3377.1648 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 : 680 0 0 0.005 0.005 4.0797 1.000 2 Bond angle potential : 923 0 1 1.913 1.913 64.260 1.000 3 Stereochemical cosine torsion poten: 410 0 15 50.985 50.985 163.35 1.000 4 Stereochemical improper torsion pot: 264 0 0 1.164 1.164 7.1630 1.000 5 Soft-sphere overlap restraints : 1305 0 0 0.004 0.004 1.9733 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) : 1392 5 15 0.741 0.741 1002.0 1.000 10 Distance restraints 2 (N-O) : 1561 6 20 0.897 0.897 1163.6 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: 90 0 1 4.064 4.064 17.530 1.000 14 Sidechain Chi_1 dihedral restraints: 76 0 0 88.690 88.690 22.844 1.000 15 Sidechain Chi_2 dihedral restraints: 48 0 1 73.284 73.284 21.547 1.000 16 Sidechain Chi_3 dihedral restraints: 22 0 0 79.008 79.008 14.350 1.000 17 Sidechain Chi_4 dihedral restraints: 8 0 0 103.972 103.972 5.1923 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 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) : 819 0 0 0.581 0.581 712.60 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: 89 20 16 42.632 77.709 89.078 1.000 26 Distance restraints 4 (SDCH-SDCH) : 95 0 1 1.573 1.573 87.657 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 0.0000 1.000 openf___224_> Open domain0.V99990004 # Heavy relative violation of each residue is written to: domain0.V99990004 # 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: 11408.8145 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 9 : Distance restraints 1 (CA-CA) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 3333 31S 77A CA CA 228 564 10.90 5.57 5.33 11.51 5.57 5.33 11.51 2 3354 32T 77A CA CA 234 564 13.68 7.99 5.69 6.06 7.99 5.69 6.06 3 3369 33H 77A CA CA 241 564 13.99 8.47 5.52 5.50 8.47 5.52 5.50 4 3405 35L 77A CA CA 256 564 12.33 7.71 4.62 4.83 7.71 4.62 4.83 5 3429 36A 77A CA CA 264 564 9.01 6.12 2.89 5.02 6.12 2.89 5.02 ------------------------------------------------------------------------------------------------- Feature 10 : Distance restraints 2 (N-O) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 4517 31S 77A N O 227 567 11.23 6.73 4.50 4.74 6.73 4.50 4.74 2 4588 36A 77A N O 263 567 11.14 6.84 4.30 4.50 6.84 4.30 4.50 3 5324 77A 31S N O 563 232 14.39 5.38 9.01 14.60 5.38 9.01 14.60 4 5325 77A 32T N O 563 239 16.36 9.74 6.62 6.05 9.74 6.62 6.05 5 5326 77A 33H N O 563 249 16.69 6.50 10.19 11.34 6.50 10.19 11.34 6 5327 77A 34A N O 563 254 12.81 8.23 4.58 4.87 8.23 4.58 4.87 ------------------------------------------------------------------------------------------------- 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 2279 2R 3C C N 17 19 50.01 -69.10 136.22 12.66 -63.00 158.40 18.10 1 3C 3C N CA 19 20 -152.09 141.80 -41.10 2 2280 3C 4G C N 23 25 63.70 78.70 71.35 1.44 -62.40 137.63 21.79 2 4G 4G N CA 25 26 -96.35 -166.10 -41.20 3 2286 9A 10P C N 59 61 -77.46 -64.50 20.63 1.24 -58.70 167.31 15.37 3 10P 10P N CA 61 62 163.24 147.20 -30.50 4 2287 10P 11S C N 66 68 92.75 -64.10 161.17 19.02 -64.10 161.17 19.02 4 11S 11S N CA 68 69 -72.08 -35.00 -35.00 5 2288 11S 12N C N 72 74 -82.46 -63.20 74.15 8.36 -63.20 74.15 8.36 5 12N 12N N CA 74 75 30.50 -41.10 -41.10 6 2289 12N 13C C N 80 82 -66.52 -63.00 4.78 0.83 -117.90 -178.04 7.81 6 13C 13C N CA 82 83 -44.34 -41.10 141.10 7 2290 13C 14H C N 86 88 -113.03 -125.60 76.15 2.64 -63.20 117.12 12.50 7 14H 14H N CA 88 89 63.69 138.80 -42.30 8 2293 16R 17A C N 112 114 -87.24 -68.20 43.34 4.09 -62.50 149.33 23.38 8 17A 17A N CA 114 115 106.37 145.30 -40.90 9 2294 17A 18C C N 117 119 157.44 -63.00 140.11 22.68 -63.00 140.11 22.68 9 18C 18C N CA 119 120 -28.72 -41.10 -41.10 10 2300 23E 24D C N 167 169 -82.84 -96.50 95.53 4.00 -63.30 112.95 15.18 10 24D 24D N CA 169 170 -151.25 114.20 -40.00 11 2307 30N 31S C N 225 227 -118.42 -136.60 28.48 1.61 -64.10 161.30 15.50 11 31S 31S N CA 227 228 173.12 151.20 -35.00 12 2308 31S 32T C N 231 233 -63.29 -63.20 14.28 1.84 -124.80 171.53 9.11 12 32T 32T N CA 233 234 -56.38 -42.10 143.50 13 2309 32T 33H C N 238 240 -66.00 -63.20 13.36 1.85 -125.60 176.22 7.64 13 33H 33H N CA 240 241 -55.36 -42.30 138.80 14 2318 41I 42R C N 300 302 -64.14 -72.10 13.39 1.16 -63.00 166.24 22.53 14 42R 42R N CA 302 303 152.67 141.90 -41.10 15 2328 51A 52G C N 372 374 -152.05 -167.20 105.19 3.91 -80.20 126.07 8.31 15 52G 52G N CA 374 375 70.51 174.60 174.10 16 2329 52G 53N C N 376 378 -72.65 -63.20 14.47 1.59 55.90 146.20 18.04 16 53N 53N N CA 378 379 -30.14 -41.10 39.50 17 2341 64P 65E C N 468 470 60.04 54.60 5.46 0.66 -63.60 148.94 25.62 17 65E 65E N CA 470 471 42.73 42.40 -40.30 18 2351 74L 75Q C N 545 547 -133.86 -121.10 13.26 0.43 -63.80 -170.19 31.61 18 75Q 75Q N CA 547 548 143.29 139.70 -40.30 19 2353 76V 77A C N 561 563 101.77 -134.00 128.09 3.22 -62.50 -143.57 34.05 19 77A 77A N CA 563 564 178.19 147.00 -40.90 20 2354 77A 78M C N 566 568 -52.22 -73.00 31.85 2.50 -63.40 152.78 21.96 20 78M 78M N CA 568 569 167.13 143.00 -40.50 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 0 11 12 45 62 57 56 73 100 69 94 << end of ENERGY. openf___224_> Open domain0.B99990004.pdb wrpdb___568_> Residues, atoms, selected atoms: 91 670 670 openf___224_> Open domain0.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2797059 2731.503 2.667 read_mo_297_> Segments, residues, atoms: 1 91 670 read_mo_298_> Segment: 1 1 91 670 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 670 670 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 670 3713 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4176 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4448 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4819 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5209 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5609 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6255 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6477 pick_re_612_> Number of MODEL atoms, selected restraints; 670 6477 iupac_m_486_> OE1/2 will be swapped: -171.6429 20 20 iupac_m_487_> NH1/2 swapped: 179.0170 26 26 iupac_m_486_> OE1/2 will be swapped: -172.1579 28 28 iupac_m_486_> OE1/2 will be swapped: 120.2737 46 46 iupac_m_485_> OD1/2 will be swapped: 92.8637 47 47 iupac_m_487_> NH1/2 swapped: 179.9720 60 60 iupac_m_486_> OE1/2 will be swapped: 127.8594 65 65 iupac_m_485_> OD1/2 will be swapped: -160.8391 90 90 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 91 Number of all, selected real atoms : 670 670 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 6477 6477 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1249 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 : 3364.5603 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 : 680 0 0 0.005 0.005 4.9027 1.000 2 Bond angle potential : 923 0 0 2.064 2.064 73.522 1.000 3 Stereochemical cosine torsion poten: 410 0 13 50.537 50.537 158.34 1.000 4 Stereochemical improper torsion pot: 264 0 0 1.216 1.216 7.6723 1.000 5 Soft-sphere overlap restraints : 1249 0 0 0.003 0.003 1.3976 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) : 1392 3 13 0.740 0.740 1007.1 1.000 10 Distance restraints 2 (N-O) : 1561 4 16 0.851 0.851 1157.6 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: 90 0 1 4.616 4.616 22.617 1.000 14 Sidechain Chi_1 dihedral restraints: 76 0 0 83.322 83.322 25.794 1.000 15 Sidechain Chi_2 dihedral restraints: 48 0 0 78.003 78.003 20.000 1.000 16 Sidechain Chi_3 dihedral restraints: 22 0 0 56.018 56.018 12.853 1.000 17 Sidechain Chi_4 dihedral restraints: 8 0 0 65.321 65.321 4.9914 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 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) : 819 0 0 0.630 0.630 712.62 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: 89 18 12 34.278 73.361 68.532 1.000 26 Distance restraints 4 (SDCH-SDCH) : 95 0 1 1.406 1.406 86.569 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 0.0000 1.000 openf___224_> Open domain0.V99990005 # Heavy relative violation of each residue is written to: domain0.V99990005 # 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: 10843.8379 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 9 : Distance restraints 1 (CA-CA) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 3333 31S 77A CA CA 228 564 10.20 5.57 4.64 10.00 5.57 4.64 10.00 2 3354 32T 77A CA CA 234 564 12.35 7.99 4.36 4.64 7.99 4.36 4.64 3 3387 34A 77A CA CA 251 564 13.76 9.00 4.76 4.72 9.00 4.76 4.72 ------------------------------------------------------------------------------------------------- Feature 10 : Distance restraints 2 (N-O) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5324 77A 31S N O 563 232 13.39 5.38 8.00 12.97 5.38 8.00 12.97 2 5325 77A 32T N O 563 239 14.99 9.74 5.25 4.80 9.74 5.25 4.80 3 5326 77A 33H N O 563 249 13.03 6.50 6.53 7.27 6.50 6.53 7.27 4 5327 77A 34A N O 563 254 13.98 8.23 5.74 6.11 8.23 5.74 6.11 ------------------------------------------------------------------------------------------------- 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 2278 1T 2R C N 6 8 -63.84 -63.00 11.51 1.50 -125.20 -179.06 7.21 1 2R 2R N CA 8 9 -29.62 -41.10 140.60 2 2286 9A 10P C N 59 61 -74.82 -64.50 16.40 0.99 -58.70 170.31 15.40 2 10P 10P N CA 61 62 159.95 147.20 -30.50 3 2287 10P 11S C N 66 68 86.44 -64.10 150.92 18.96 -64.10 150.92 18.96 3 11S 11S N CA 68 69 -45.62 -35.00 -35.00 4 2288 11S 12N C N 72 74 -87.48 -119.90 86.48 3.11 -63.20 100.89 11.44 4 12N 12N N CA 74 75 56.82 137.00 -41.10 5 2290 13C 14H C N 86 88 -91.14 -67.60 64.17 5.53 -63.20 125.75 14.20 5 14H 14H N CA 88 89 80.31 140.00 -42.30 6 2300 23E 24D C N 167 169 -81.09 -96.50 97.20 4.07 -63.30 111.26 14.86 6 24D 24D N CA 169 170 -149.83 114.20 -40.00 7 2307 30N 31S C N 225 227 -138.08 -136.60 34.26 1.71 -64.10 157.96 16.76 7 31S 31S N CA 227 228 -174.57 151.20 -35.00 8 2308 31S 32T C N 231 233 -60.62 -63.20 9.39 1.05 -124.80 177.39 9.43 8 32T 32T N CA 233 234 -51.13 -42.10 143.50 9 2310 33H 34A C N 248 250 -58.77 -62.50 13.79 2.11 -134.00 175.74 10.84 9 34A 34A N CA 250 251 -54.18 -40.90 147.00 10 2319 42R 43A C N 311 313 90.48 55.40 75.01 2.74 -62.50 153.52 30.01 10 43A 43A N CA 313 314 -28.11 38.20 -40.90 11 2327 50N 51A C N 367 369 -66.02 -68.20 14.16 1.06 -62.50 172.24 28.06 11 51A 51A N CA 369 370 131.31 145.30 -40.90 12 2328 51A 52G C N 372 374 72.58 78.70 40.82 0.91 -80.20 164.20 12.08 12 52G 52G N CA 374 375 -125.74 -166.10 174.10 13 2341 64P 65E C N 468 470 54.15 54.60 8.19 0.59 -63.60 148.74 25.51 13 65E 65E N CA 470 471 50.57 42.40 -40.30 14 2350 73D 74L C N 537 539 178.29 -63.50 130.06 23.96 -108.50 151.01 7.23 14 74L 74L N CA 539 540 -95.42 -41.20 132.50 15 2351 74L 75Q C N 545 547 -96.17 -73.00 46.40 2.68 -63.80 142.53 22.69 15 75Q 75Q N CA 547 548 -179.10 140.70 -40.30 16 2353 76V 77A C N 561 563 -73.34 -68.20 46.03 3.53 -62.50 128.51 21.61 16 77A 77A N CA 563 564 -168.95 145.30 -40.90 17 2354 77A 78M C N 566 568 -52.60 -73.00 38.33 2.95 -63.40 144.46 20.75 17 78M 78M N CA 568 569 175.45 143.00 -40.50 18 2366 89D 90D C N 653 655 -62.34 -63.30 7.03 0.81 -96.50 164.74 6.94 18 90D 90D N CA 655 656 -46.96 -40.00 114.20 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 0 5 9 44 51 60 61 69 95 86 95 << end of ENERGY. openf___224_> Open domain0.B99990005.pdb wrpdb___568_> Residues, atoms, selected atoms: 91 670 670 >> Summary of successfully produced models: Filename molpdf ---------------------------------------- domain0.B99990001.pdb 3365.32886 domain0.B99990002.pdb 3689.85352 domain0.B99990003.pdb 3420.86133 domain0.B99990004.pdb 3377.16479 domain0.B99990005.pdb 3364.56030 Dynamically allocated memory at finish [B,KiB,MiB]: 2797039 2731.483 2.667 Starting time : 2019/05/05 16:19:19 Closing time : 2019/05/05 16:20:30 Total CPU time [seconds] : 34.29