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 16:28:11 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_compro4.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_compro4.pir Total number of alignment positions: 175 # 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 ---------------------------------------------------- 55 1 2 55 49 T K 10.226 56 1 2 56 50 F I 8.560 90 1 2 89 73 I D 8.941 55 1 3 55 49 T K 10.048 56 1 3 56 50 F I 7.611 59 1 3 59 53 D V 6.595 79 1 3 78 71 K I 9.598 61 2 3 55 55 E E 6.151 79 2 3 72 71 L I 9.171 90 2 3 73 72 D Q 11.655 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 ---------------------------------------------- 47 1 47 70 A R 10.988 47 2 45 64 A R 12.279 47 3 45 65 A R 12.022 76 1 75 78 R I 13.158 76 2 69 72 R I 13.207 79 1 78 89 I E 8.069 79 3 71 72 I E 13.214 90 2 73 74 E D 10.413 99 1 98 112 T H 16.375 99 2 82 95 T H 16.444 99 3 81 95 T H 17.246 171 1 159 163 D T 13.673 171 2 141 145 D T 13.385 171 3 142 146 D T 13.511 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: 511 159 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 make_re_422_> Number of previous, current restraints : 3244 4025 make_re_423_> Number of previous, current selected restraints: 3149 3930 make_re_417_> Restraint type to be calculated: DISTANCE 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 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2182900 2131.738 2.082 make_re_422_> Number of previous, current restraints : 4025 4983 make_re_423_> Number of previous, current selected restraints: 3930 4888 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2707188 2643.738 2.582 make_re_422_> Number of previous, current restraints : 4983 5834 make_re_423_> Number of previous, current selected restraints: 4888 5739 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2772724 2707.738 2.644 make_re_422_> Number of previous, current restraints : 5834 5920 make_re_423_> Number of previous, current selected restraints: 5739 5825 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 : 5920 5920 make_re_423_> Number of previous, current selected restraints: 5825 5825 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 5920 5920 make_re_423_> Number of previous, current selected restraints: 5825 5825 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 5920 5920 make_re_423_> Number of previous, current selected restraints: 5825 5825 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 5920 5920 make_re_423_> Number of previous, current selected restraints: 5825 5825 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 : 5920 5920 make_re_423_> Number of previous, current selected restraints: 5825 5825 rmdupl__427_> 539 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 5920 5286 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 : 5286 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 5286 5286 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 3692 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4025 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4207 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4478 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4785 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4878 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2797039 2731.483 2.667 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5024 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5282 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5286 iupac_m_485_> OD1/2 will be swapped: 133.4234 24 24 iupac_m_487_> NH1/2 swapped: 175.0369 26 26 iupac_m_486_> OE1/2 will be swapped: -161.1687 46 46 iupac_m_485_> OD1/2 will be swapped: 145.7215 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 : 5286 5286 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1051 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 : 3089.4460 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 0.004 0.004 2.8339 1.000 2 Bond angle potential : 923 0 0 1.717 1.717 51.242 1.000 3 Stereochemical cosine torsion poten: 410 0 23 54.376 54.376 192.64 1.000 4 Stereochemical improper torsion pot: 264 0 0 1.057 1.057 6.0155 1.000 5 Soft-sphere overlap restraints : 1051 0 0 0.003 0.003 0.89766 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) : 781 0 15 1.392 1.392 761.46 1.000 10 Distance restraints 2 (N-O) : 958 1 15 1.382 1.382 914.47 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 3.190 3.190 10.803 1.000 14 Sidechain Chi_1 dihedral restraints: 76 0 1 78.990 78.990 25.575 1.000 15 Sidechain Chi_2 dihedral restraints: 48 0 0 76.903 76.903 29.112 1.000 16 Sidechain Chi_3 dihedral restraints: 22 0 0 88.547 88.547 13.850 1.000 17 Sidechain Chi_4 dihedral restraints: 8 0 0 120.123 120.123 6.6855 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) : 851 0 9 1.167 1.167 865.88 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 27 18 43.357 98.948 114.79 1.000 26 Distance restraints 4 (SDCH-SDCH) : 86 0 1 2.486 2.486 93.189 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: 12337.3564 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 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 -150.11 -167.20 17.80 0.26 82.20 -154.42 15.35 1 4G 4G N CA 25 26 169.62 174.60 8.50 2 2282 5C 6G C N 33 35 -128.58 -167.20 66.49 1.78 82.20 -173.44 14.55 2 6G 6G N CA 35 36 120.47 174.60 8.50 3 2286 9A 10P C N 59 61 -69.67 -58.70 26.87 1.58 -64.50 153.25 11.71 3 10P 10P N CA 61 62 -5.97 -30.50 147.20 4 2287 10P 11S C N 66 68 80.30 56.90 55.12 2.25 -64.10 146.00 19.29 4 11S 11S N CA 68 69 -13.50 36.40 -35.00 5 2290 13C 14H C N 86 88 -130.81 -125.60 52.52 2.09 -63.20 145.50 15.47 5 14H 14H N CA 88 89 86.53 138.80 -42.30 6 2291 14H 15A C N 96 98 -177.58 -134.00 44.24 1.20 -62.50 -159.28 38.97 6 15A 15A N CA 98 99 154.64 147.00 -40.90 7 2297 20E 21R C N 139 141 -93.19 -125.20 40.42 1.19 -63.00 159.89 19.74 7 21R 21R N CA 141 142 115.91 140.60 -41.10 8 2298 21R 22I C N 150 152 -130.22 -120.60 10.32 0.81 -63.40 -177.19 28.10 8 22I 22I N CA 152 153 126.56 130.30 -43.60 9 2300 23E 24D C N 167 169 179.26 -96.50 96.23 3.92 54.50 127.60 16.08 9 24D 24D N CA 169 170 67.70 114.20 40.90 10 2301 24D 25P C N 175 177 -74.89 -58.70 30.28 1.80 -64.50 152.47 11.93 10 25P 25P N CA 177 178 -4.91 -30.50 147.20 11 2302 25P 26R C N 182 184 100.79 -125.20 174.99 5.21 -63.00 176.50 25.09 11 26R 26R N CA 184 185 -106.88 140.60 -41.10 12 2306 29I 30N C N 217 219 64.60 55.90 88.21 6.82 -63.20 -148.62 33.34 12 30N 30N N CA 219 220 127.28 39.50 -41.10 13 2307 30N 31S C N 225 227 -67.29 -72.40 45.03 2.48 -64.10 142.70 10.15 13 31S 31S N CA 227 228 107.66 152.40 -35.00 14 2308 31S 32T C N 231 233 -146.39 -124.80 25.91 0.95 -63.20 -179.60 28.52 14 32T 32T N CA 233 234 157.83 143.50 -42.10 15 2321 44P 45S C N 323 325 57.37 -72.40 129.84 9.40 -64.10 -152.66 14.69 15 45S 45S N CA 325 326 156.96 152.40 -35.00 16 2322 45S 46E C N 329 331 -87.88 -117.80 63.79 2.48 -63.60 123.18 15.22 16 46E 46E N CA 331 332 80.46 136.80 -40.30 17 2328 51A 52G C N 372 374 -91.78 -80.20 19.97 1.32 82.20 -130.73 7.84 17 52G 52G N CA 374 375 157.82 174.10 8.50 18 2333 56A 57P C N 406 408 -57.62 -64.50 25.15 1.56 -58.70 153.50 12.77 18 57P 57P N CA 408 409 123.00 147.20 -30.50 19 2335 58S 59D C N 419 421 -95.35 -70.90 24.64 1.76 -63.30 169.71 22.99 19 59D 59D N CA 421 422 153.34 150.30 -40.00 20 2337 60R 61A C N 438 440 161.49 -134.00 72.25 1.65 -62.50 -165.11 38.87 20 61A 61A N CA 440 441 179.53 147.00 -40.90 21 2338 61A 62F C N 443 445 -90.80 -71.40 26.77 2.34 -63.20 168.83 21.65 21 62F 62F N CA 445 446 122.25 140.70 -44.30 22 2339 62F 63T C N 454 456 -137.82 -124.80 14.75 0.58 -63.20 -176.67 28.40 22 63T 63T N CA 456 457 150.44 143.50 -42.10 23 2341 64P 65E C N 468 470 -166.84 -117.80 54.19 1.59 -63.60 -169.72 31.01 23 65E 65E N CA 470 471 159.86 136.80 -40.30 24 2344 67V 68M C N 490 492 -128.44 -125.60 6.37 0.34 -63.40 -173.02 23.79 24 68M 68M N CA 492 493 134.80 140.50 -40.50 25 2345 68M 69C C N 498 500 -121.39 -117.90 47.51 1.92 -63.00 146.92 15.27 25 69C 69C N CA 500 501 93.72 141.10 -41.10 26 2346 69C 70M C N 504 506 -101.43 -63.40 81.78 10.13 -63.40 81.78 10.13 26 70M 70M N CA 506 507 31.89 -40.50 -40.50 27 2347 70M 71H C N 512 514 -91.42 -67.60 89.03 7.49 -63.20 100.56 11.11 27 71H 71H N CA 514 515 54.22 140.00 -42.30 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 6 5 38 42 40 57 46 69 85 81 << 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 3692 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4025 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4207 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4478 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4785 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4878 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5024 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5282 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5286 iupac_m_487_> NH1/2 swapped: 179.0040 2 2 iupac_m_487_> NH1/2 swapped: -177.1348 16 16 iupac_m_487_> NH1/2 swapped: 178.5821 21 21 iupac_m_487_> NH1/2 swapped: 177.8989 60 60 iupac_m_485_> OD1/2 will be swapped: -174.7221 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 : 5286 5286 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1073 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 : 3122.8315 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 0.004 0.004 2.8752 1.000 2 Bond angle potential : 923 0 0 1.726 1.726 54.019 1.000 3 Stereochemical cosine torsion poten: 410 0 21 52.065 52.065 168.38 1.000 4 Stereochemical improper torsion pot: 264 0 0 0.983 0.983 5.5694 1.000 5 Soft-sphere overlap restraints : 1073 0 0 0.002 0.002 0.65307 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) : 781 2 17 1.476 1.476 781.58 1.000 10 Distance restraints 2 (N-O) : 958 4 31 1.557 1.557 987.94 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 3.598 3.598 13.737 1.000 14 Sidechain Chi_1 dihedral restraints: 76 0 0 81.380 81.380 19.798 1.000 15 Sidechain Chi_2 dihedral restraints: 48 0 0 71.259 71.259 25.220 1.000 16 Sidechain Chi_3 dihedral restraints: 22 0 0 79.588 79.588 14.371 1.000 17 Sidechain Chi_4 dihedral restraints: 8 0 0 44.413 44.413 6.3451 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) : 851 0 9 1.132 1.132 866.12 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 33 17 35.252 102.041 85.896 1.000 26 Distance restraints 4 (SDCH-SDCH) : 86 0 1 2.035 2.035 90.330 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: 12721.5596 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 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 4174 81I 77A N O 588 567 5.56 2.99 2.58 7.24 2.99 2.58 7.24 ------------------------------------------------------------------------------------------------- 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 -135.62 -167.20 44.51 0.99 82.20 -164.13 15.09 1 4G 4G N CA 25 26 143.23 174.60 8.50 2 2282 5C 6G C N 33 35 -117.33 -80.20 55.40 3.85 82.20 -156.92 15.82 2 6G 6G N CA 35 36 132.98 174.10 8.50 3 2286 9A 10P C N 59 61 -68.72 -58.70 28.14 1.69 -64.50 151.46 11.53 3 10P 10P N CA 61 62 -4.21 -30.50 147.20 4 2287 10P 11S C N 66 68 77.76 56.90 46.03 1.90 -64.10 145.07 19.31 4 11S 11S N CA 68 69 -4.64 36.40 -35.00 5 2291 14H 15A C N 96 98 -67.18 -68.20 2.28 0.22 -62.50 171.82 28.39 5 15A 15A N CA 98 99 147.35 145.30 -40.90 6 2297 20E 21R C N 139 141 -94.58 -125.20 54.51 1.84 -63.00 140.21 17.04 6 21R 21R N CA 141 142 95.51 140.60 -41.10 7 2298 21R 22I C N 150 152 -144.31 -120.60 23.87 1.74 -63.40 -170.74 28.91 7 22I 22I N CA 152 153 127.49 130.30 -43.60 8 2300 23E 24D C N 167 169 -112.99 -96.50 19.01 0.77 54.50 179.24 16.86 8 24D 24D N CA 169 170 104.73 114.20 40.90 9 2301 24D 25P C N 175 177 -69.11 -58.70 15.17 1.04 -64.50 166.73 12.69 9 25P 25P N CA 177 178 -19.47 -30.50 147.20 10 2304 27T 28E C N 200 202 -63.89 -117.80 55.63 1.74 -63.60 163.37 21.77 10 28E 28E N CA 202 203 123.07 136.80 -40.30 11 2306 29I 30N C N 217 219 -113.35 -119.90 84.34 3.98 -63.20 109.93 16.56 11 30N 30N N CA 219 220 -138.92 137.00 -41.10 12 2307 30N 31S C N 225 227 -60.82 -72.40 18.02 0.83 -64.10 173.62 12.78 12 31S 31S N CA 227 228 138.59 152.40 -35.00 13 2308 31S 32T C N 231 233 -69.12 -78.10 9.02 0.53 -63.20 169.03 22.07 13 32T 32T N CA 233 234 148.97 149.80 -42.10 14 2309 32T 33H C N 238 240 -67.16 -63.20 9.08 1.39 -125.60 -179.55 7.79 14 33H 33H N CA 240 241 -50.47 -42.30 138.80 15 2322 45S 46E C N 329 331 -120.07 -117.80 62.33 3.17 -63.60 127.95 14.85 15 46E 46E N CA 331 332 74.51 136.80 -40.30 16 2327 50N 51A C N 367 369 -66.93 -62.50 7.34 1.43 -134.00 179.28 11.05 16 51A 51A N CA 369 370 -46.75 -40.90 147.00 17 2328 51A 52G C N 372 374 81.01 78.70 43.59 1.15 82.20 141.87 6.83 17 52G 52G N CA 374 375 150.37 -166.10 8.50 18 2334 57P 58S C N 413 415 -62.69 -64.10 1.64 0.16 -72.40 172.03 10.46 18 58S 58S N CA 415 416 -35.85 -35.00 152.40 19 2335 58S 59D C N 419 421 -83.97 -96.50 69.58 2.93 -63.30 88.22 9.82 19 59D 59D N CA 421 422 45.76 114.20 -40.00 20 2337 60R 61A C N 438 440 -53.77 -68.20 28.58 1.85 -62.50 161.77 26.95 20 61A 61A N CA 440 441 120.64 145.30 -40.90 21 2338 61A 62F C N 443 445 159.34 -124.20 88.58 2.34 -63.20 -172.39 33.66 21 62F 62F N CA 445 446 -171.97 143.30 -44.30 22 2339 62F 63T C N 454 456 -107.58 -124.80 41.15 1.33 -63.20 154.73 17.30 22 63T 63T N CA 456 457 106.13 143.50 -42.10 23 2341 64P 65E C N 468 470 -92.35 -117.80 62.21 2.53 -63.60 123.73 15.10 23 65E 65E N CA 470 471 80.04 136.80 -40.30 24 2342 65E 66S C N 477 479 -170.91 -136.60 42.01 1.28 -64.10 -176.21 21.03 24 66S 66S N CA 479 480 175.43 151.20 -35.00 25 2343 66S 67V C N 483 485 -63.54 -62.40 3.56 0.52 -125.40 -178.23 10.19 25 67V 67V N CA 485 486 -45.77 -42.40 143.30 26 2344 67V 68M C N 490 492 -82.76 -73.00 13.64 0.87 -63.40 168.10 26.63 26 68M 68M N CA 492 493 152.52 143.00 -40.50 27 2345 68M 69C C N 498 500 -106.55 -117.90 50.80 2.15 -63.00 135.47 19.78 27 69C 69C N CA 500 501 -169.38 141.10 -41.10 28 2346 69C 70M C N 504 506 -67.01 -73.00 7.80 0.50 -63.40 178.55 26.38 28 70M 70M N CA 506 507 138.01 143.00 -40.50 29 2347 70M 71H C N 512 514 -119.62 -125.60 61.19 2.21 -63.20 132.79 14.17 29 71H 71H N CA 514 515 77.91 138.80 -42.30 30 2348 71H 72V C N 522 524 -85.26 -125.40 45.23 1.22 -62.40 166.44 19.83 30 72V 72V N CA 524 525 122.46 143.30 -42.40 31 2349 72V 73D C N 529 531 67.37 54.50 45.67 2.46 -63.30 135.83 22.87 31 73D 73D N CA 531 532 -2.92 40.90 -40.00 32 2353 76V 77A C N 561 563 -77.51 -68.20 25.91 1.77 -62.50 150.37 25.41 32 77A 77A N CA 563 564 169.49 145.30 -40.90 33 2354 77A 78M C N 566 568 68.56 56.30 47.71 1.36 -63.40 135.14 26.57 33 78M 78M N CA 568 569 -11.31 34.80 -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 8 8 32 47 60 49 63 62 67 93 << 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 3692 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4025 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4207 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4478 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4785 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4878 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5024 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5282 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5286 iupac_m_487_> NH1/2 swapped: -179.1741 16 16 iupac_m_487_> NH1/2 swapped: -179.6961 21 21 iupac_m_486_> OE1/2 will be swapped: -161.0782 23 23 iupac_m_485_> OD1/2 will be swapped: 143.3918 24 24 iupac_m_487_> NH1/2 swapped: -179.6620 42 42 iupac_m_486_> OE1/2 will be swapped: 178.1825 46 46 iupac_m_487_> NH1/2 swapped: -176.5907 60 60 iupac_m_485_> OD1/2 will be swapped: 134.5333 89 89 >> 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 : 5286 5286 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1083 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 : 3035.1045 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 0.003 0.003 1.7318 1.000 2 Bond angle potential : 923 0 0 1.771 1.771 53.757 1.000 3 Stereochemical cosine torsion poten: 410 0 17 51.170 51.170 169.14 1.000 4 Stereochemical improper torsion pot: 264 0 0 1.007 1.007 5.4682 1.000 5 Soft-sphere overlap restraints : 1083 0 0 0.002 0.002 0.55345 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) : 781 1 17 1.393 1.393 761.32 1.000 10 Distance restraints 2 (N-O) : 958 2 25 1.398 1.398 942.66 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 3.781 3.781 15.172 1.000 14 Sidechain Chi_1 dihedral restraints: 76 0 0 87.186 87.186 23.915 1.000 15 Sidechain Chi_2 dihedral restraints: 48 0 0 71.541 71.541 21.412 1.000 16 Sidechain Chi_3 dihedral restraints: 22 0 0 76.834 76.834 13.638 1.000 17 Sidechain Chi_4 dihedral restraints: 8 0 0 89.470 89.470 4.9741 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) : 851 0 9 1.152 1.152 865.52 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 28 12 32.512 101.326 60.496 1.000 26 Distance restraints 4 (SDCH-SDCH) : 86 0 1 2.542 2.542 95.354 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: 12251.8232 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 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 -143.90 -167.20 45.30 1.30 82.20 -175.28 14.23 1 4G 4G N CA 25 26 135.75 174.60 8.50 2 2282 5C 6G C N 33 35 -122.05 -80.20 62.81 4.35 82.20 -164.14 15.27 2 6G 6G N CA 35 36 127.26 174.10 8.50 3 2290 13C 14H C N 86 88 -136.31 -125.60 14.73 0.67 -63.20 -174.04 19.94 3 14H 14H N CA 88 89 128.69 138.80 -42.30 4 2291 14H 15A C N 96 98 157.24 -134.00 68.81 2.18 -62.50 -140.03 43.34 4 15A 15A N CA 98 99 149.65 147.00 -40.90 5 2297 20E 21R C N 139 141 -100.32 -125.20 43.88 1.47 -63.00 150.26 18.09 5 21R 21R N CA 141 142 104.45 140.60 -41.10 6 2298 21R 22I C N 150 152 -131.82 -120.60 19.02 0.78 -63.40 -176.07 32.66 6 22I 22I N CA 152 153 145.66 130.30 -43.60 7 2300 23E 24D C N 167 169 -174.67 -96.50 85.49 3.48 54.50 136.43 17.45 7 24D 24D N CA 169 170 79.60 114.20 40.90 8 2304 27T 28E C N 200 202 159.36 -117.80 84.54 2.72 -63.60 -144.72 35.95 8 28E 28E N CA 202 203 153.66 136.80 -40.30 9 2305 28E 29I C N 209 211 -66.19 -63.40 5.02 0.92 -120.60 -173.80 8.65 9 29I 29I N CA 211 212 -47.77 -43.60 130.30 10 2306 29I 30N C N 217 219 -67.07 -71.20 4.95 0.28 -63.20 178.88 22.58 10 30N 30N N CA 219 220 140.07 142.80 -41.10 11 2307 30N 31S C N 225 227 -60.80 -72.40 33.72 1.63 -64.10 155.78 11.49 11 31S 31S N CA 227 228 120.74 152.40 -35.00 12 2308 31S 32T C N 231 233 -160.70 -124.80 42.76 1.57 -63.20 179.89 29.24 12 32T 32T N CA 233 234 166.73 143.50 -42.10 13 2320 43A 44P C N 316 318 -59.77 -58.70 3.17 0.35 -64.50 179.38 13.64 13 44P 44P N CA 318 319 -33.48 -30.50 147.20 14 2321 44P 45S C N 323 325 -161.60 -136.60 25.10 0.94 -64.10 -162.63 21.32 14 45S 45S N CA 325 326 153.39 151.20 -35.00 15 2324 47D 48N C N 346 348 -61.06 -119.90 67.38 3.49 55.90 175.12 9.87 15 48N 48N N CA 348 349 169.84 137.00 39.50 16 2327 50N 51A C N 367 369 -64.78 -62.50 3.50 0.69 -134.00 -176.95 11.29 16 51A 51A N CA 369 370 -43.54 -40.90 147.00 17 2328 51A 52G C N 372 374 92.09 78.70 26.12 0.40 82.20 163.27 8.42 17 52G 52G N CA 374 375 171.47 -166.10 8.50 18 2334 57P 58S C N 413 415 -66.61 -64.10 14.95 0.96 -72.40 172.76 9.96 18 58S 58S N CA 415 416 -20.26 -35.00 152.40 19 2335 58S 59D C N 419 421 -77.20 -63.30 65.87 7.40 -63.30 65.87 7.40 19 59D 59D N CA 421 422 24.38 -40.00 -40.00 20 2337 60R 61A C N 438 440 -102.82 -134.00 41.68 1.17 -62.50 165.24 25.42 20 61A 61A N CA 440 441 119.34 147.00 -40.90 21 2338 61A 62F C N 443 445 -170.10 -124.20 100.48 3.40 -63.20 135.35 24.41 21 62F 62F N CA 445 446 -127.31 143.30 -44.30 22 2341 64P 65E C N 468 470 -68.98 -69.30 29.22 2.22 -63.60 153.68 20.20 22 65E 65E N CA 470 471 113.28 142.50 -40.30 23 2342 65E 66S C N 477 479 -171.93 -136.60 36.34 1.24 -64.10 -162.64 22.08 23 66S 66S N CA 479 480 159.70 151.20 -35.00 24 2344 67V 68M C N 490 492 -152.32 -125.60 44.61 1.47 -63.40 168.63 32.01 24 68M 68M N CA 492 493 176.22 140.50 -40.50 25 2345 68M 69C C N 498 500 -94.26 -117.90 24.54 0.73 -63.00 178.39 19.85 25 69C 69C N CA 500 501 134.53 141.10 -41.10 26 2347 70M 71H C N 512 514 61.59 56.30 16.18 1.16 -63.20 142.02 24.39 26 71H 71H N CA 514 515 25.51 40.80 -42.30 27 2362 85L 86T C N 625 627 -124.89 -124.80 3.03 0.13 -63.20 -177.86 27.44 27 86T 86T N CA 627 628 146.52 143.50 -42.10 28 2363 86T 87G C N 632 634 -60.71 -62.40 12.88 2.01 82.20 147.61 11.00 28 87G 87G N CA 634 635 -28.44 -41.20 8.50 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 10 10 45 46 58 39 56 74 69 79 << 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 3692 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4025 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4207 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4478 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4785 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4878 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5024 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5282 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5286 iupac_m_487_> NH1/2 swapped: -179.8333 16 16 iupac_m_487_> NH1/2 swapped: 179.8242 21 21 iupac_m_485_> OD1/2 will be swapped: 134.5992 24 24 iupac_m_486_> OE1/2 will be swapped: 99.1752 28 28 iupac_m_486_> OE1/2 will be swapped: 179.2824 46 46 iupac_m_485_> OD1/2 will be swapped: 170.0790 59 59 iupac_m_487_> NH1/2 swapped: -177.5828 60 60 iupac_m_485_> OD1/2 will be swapped: 175.0730 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 : 5286 5286 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1076 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 : 2997.0886 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 0.003 0.003 1.8322 1.000 2 Bond angle potential : 923 0 0 1.720 1.720 51.381 1.000 3 Stereochemical cosine torsion poten: 410 0 21 53.502 53.502 175.33 1.000 4 Stereochemical improper torsion pot: 264 0 0 0.825 0.825 3.5822 1.000 5 Soft-sphere overlap restraints : 1076 0 0 0.002 0.002 0.77122 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) : 781 1 12 1.386 1.386 759.12 1.000 10 Distance restraints 2 (N-O) : 958 2 15 1.415 1.415 911.15 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 3.612 3.612 13.845 1.000 14 Sidechain Chi_1 dihedral restraints: 76 0 0 88.760 88.760 22.612 1.000 15 Sidechain Chi_2 dihedral restraints: 48 0 0 73.200 73.200 21.267 1.000 16 Sidechain Chi_3 dihedral restraints: 22 0 0 92.338 92.338 14.769 1.000 17 Sidechain Chi_4 dihedral restraints: 8 0 0 56.085 56.085 5.4193 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) : 851 0 9 1.146 1.146 861.96 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 25 15 33.230 91.492 59.091 1.000 26 Distance restraints 4 (SDCH-SDCH) : 86 0 1 2.813 2.813 94.960 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: 11631.9111 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 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 4072 75Q 60R N O 547 439 13.19 7.58 5.61 4.80 7.58 5.61 4.80 ------------------------------------------------------------------------------------------------- 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 -131.67 -167.20 52.04 1.21 82.20 -165.70 15.05 1 4G 4G N CA 25 26 136.57 174.60 8.50 2 2282 5C 6G C N 33 35 -125.54 -167.20 68.14 1.75 82.20 -170.88 14.76 2 6G 6G N CA 35 36 120.68 174.60 8.50 3 2286 9A 10P C N 59 61 -70.27 -58.70 24.25 1.42 -64.50 156.49 11.98 3 10P 10P N CA 61 62 -9.19 -30.50 147.20 4 2287 10P 11S C N 66 68 76.29 56.90 45.67 1.87 -64.10 143.57 19.11 4 11S 11S N CA 68 69 -4.95 36.40 -35.00 5 2290 13C 14H C N 86 88 62.96 56.30 7.39 0.93 -63.20 149.33 25.63 5 14H 14H N CA 88 89 37.60 40.80 -42.30 6 2291 14H 15A C N 96 98 -85.12 -68.20 40.33 2.69 -62.50 139.04 23.96 6 15A 15A N CA 98 99 -178.09 145.30 -40.90 7 2293 16R 17A C N 112 114 56.41 55.40 3.21 0.28 -134.00 -160.14 10.61 7 17A 17A N CA 114 115 41.24 38.20 147.00 8 2297 20E 21R C N 139 141 -103.25 -125.20 46.29 1.67 -63.00 146.57 17.46 8 21R 21R N CA 141 142 99.84 140.60 -41.10 9 2298 21R 22I C N 150 152 -73.31 -97.30 24.81 1.13 -63.40 177.42 28.73 9 22I 22I N CA 152 153 133.54 127.20 -43.60 10 2300 23E 24D C N 167 169 175.85 54.50 123.73 13.13 54.50 123.73 13.13 10 24D 24D N CA 169 170 16.78 40.90 40.90 11 2305 28E 29I C N 209 211 -29.70 -97.30 68.57 2.92 -120.60 91.29 6.59 11 29I 29I N CA 211 212 138.65 127.20 130.30 12 2306 29I 30N C N 217 219 -57.66 -71.20 23.52 1.85 -63.20 156.97 19.33 12 30N 30N N CA 219 220 162.03 142.80 -41.10 13 2307 30N 31S C N 225 227 58.06 56.90 8.88 0.67 -64.10 146.14 19.06 13 31S 31S N CA 227 228 45.21 36.40 -35.00 14 2322 45S 46E C N 329 331 -60.94 -69.30 31.87 2.13 -63.60 152.07 20.42 14 46E 46E N CA 331 332 111.75 142.50 -40.30 15 2324 47D 48N C N 346 348 -123.51 -119.90 15.15 0.76 55.90 -162.41 16.90 15 48N 48N N CA 348 349 122.29 137.00 39.50 16 2328 51A 52G C N 372 374 -106.70 -80.20 38.58 2.70 82.20 -140.47 17.08 16 52G 52G N CA 374 375 146.05 174.10 8.50 17 2332 55H 56A C N 401 403 -65.88 -62.50 4.25 0.86 -68.20 171.24 13.89 17 56A 56A N CA 403 404 -43.47 -40.90 145.30 18 2335 58S 59D C N 419 421 148.42 -96.50 136.56 5.67 -63.30 -161.30 33.35 18 59D 59D N CA 421 422 -172.27 114.20 -40.00 19 2337 60R 61A C N 438 440 -157.48 -134.00 31.91 0.92 -62.50 177.97 34.21 19 61A 61A N CA 440 441 168.60 147.00 -40.90 20 2339 62F 63T C N 454 456 -96.72 -78.10 30.35 1.89 -63.20 171.25 19.92 20 63T 63T N CA 456 457 125.83 149.80 -42.10 21 2341 64P 65E C N 468 470 -126.44 -117.80 17.36 0.66 -63.60 179.22 27.44 21 65E 65E N CA 470 471 151.85 136.80 -40.30 22 2344 67V 68M C N 490 492 -68.16 -73.00 27.96 1.97 -63.40 149.04 22.62 22 68M 68M N CA 492 493 170.54 143.00 -40.50 23 2345 68M 69C C N 498 500 -70.86 -69.10 60.90 3.67 -63.00 116.49 14.76 23 69C 69C N CA 500 501 -157.32 141.80 -41.10 24 2346 69C 70M C N 504 506 -50.23 -73.00 39.36 2.45 -63.40 151.97 23.73 24 70M 70M N CA 506 507 110.89 143.00 -40.50 25 2347 70M 71H C N 512 514 -121.07 -125.60 85.46 3.16 -63.20 111.89 11.90 25 71H 71H N CA 514 515 53.46 138.80 -42.30 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 10 34 57 56 62 53 82 85 65 << 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 3692 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4025 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4207 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4478 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4785 pick_re_612_> Number of MODEL atoms, selected restraints; 670 4878 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5024 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5282 pick_re_612_> Number of MODEL atoms, selected restraints; 670 5286 iupac_m_487_> NH1/2 swapped: 179.7093 2 2 iupac_m_487_> NH1/2 swapped: 178.5669 16 16 iupac_m_486_> OE1/2 will be swapped: 175.9046 23 23 iupac_m_485_> OD1/2 will be swapped: 142.1490 24 24 iupac_m_487_> NH1/2 swapped: -177.2118 42 42 iupac_m_486_> OE1/2 will be swapped: 172.2838 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 : 5286 5286 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1079 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 : 3024.9517 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 0.003 0.003 1.5253 1.000 2 Bond angle potential : 923 0 0 1.542 1.542 44.123 1.000 3 Stereochemical cosine torsion poten: 410 0 27 54.748 54.748 190.65 1.000 4 Stereochemical improper torsion pot: 264 0 0 0.886 0.886 4.3525 1.000 5 Soft-sphere overlap restraints : 1079 0 0 0.002 0.002 0.47038 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) : 781 1 13 1.372 1.372 760.83 1.000 10 Distance restraints 2 (N-O) : 958 2 15 1.358 1.358 912.07 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 3.605 3.605 13.797 1.000 14 Sidechain Chi_1 dihedral restraints: 76 0 0 81.088 81.088 18.378 1.000 15 Sidechain Chi_2 dihedral restraints: 48 0 0 83.075 83.075 25.251 1.000 16 Sidechain Chi_3 dihedral restraints: 22 0 0 78.827 78.827 12.063 1.000 17 Sidechain Chi_4 dihedral restraints: 8 0 0 113.403 113.403 5.9557 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) : 851 0 10 1.124 1.124 865.82 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 30 16 37.536 104.539 73.048 1.000 26 Distance restraints 4 (SDCH-SDCH) : 86 0 1 2.267 2.267 96.621 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: 12168.2012 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 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 -65.36 -63.00 8.37 1.20 -117.90 177.71 7.65 1 3C 3C N CA 19 20 -49.13 -41.10 141.10 2 2280 3C 4G C N 23 25 89.76 78.70 55.81 1.15 82.20 130.91 6.73 2 4G 4G N CA 25 26 139.19 -166.10 8.50 3 2282 5C 6G C N 33 35 -118.62 -80.20 60.48 4.13 82.20 -161.32 15.50 3 6G 6G N CA 35 36 127.39 174.10 8.50 4 2286 9A 10P C N 59 61 -65.22 -58.70 15.98 0.94 -64.50 163.11 12.21 4 10P 10P N CA 61 62 -15.91 -30.50 147.20 5 2287 10P 11S C N 66 68 72.87 56.90 44.27 1.82 -64.10 140.25 18.67 5 11S 11S N CA 68 69 -4.88 36.40 -35.00 6 2290 13C 14H C N 86 88 -177.33 -125.60 73.76 1.83 -63.20 170.25 28.30 6 14H 14H N CA 88 89 -168.62 138.80 -42.30 7 2291 14H 15A C N 96 98 -155.80 -134.00 32.28 1.02 -62.50 175.21 33.67 7 15A 15A N CA 98 99 170.80 147.00 -40.90 8 2292 15A 16R C N 101 103 77.95 57.30 67.54 3.33 -125.20 -130.96 12.62 8 16R 16R N CA 103 104 -26.30 38.00 140.60 9 2297 20E 21R C N 139 141 -102.25 -125.20 36.98 1.19 -63.00 157.67 18.97 9 21R 21R N CA 141 142 111.60 140.60 -41.10 10 2298 21R 22I C N 150 152 -124.58 -120.60 10.33 0.74 -63.40 175.39 27.01 10 22I 22I N CA 152 153 120.77 130.30 -43.60 11 2300 23E 24D C N 167 169 -56.55 -70.90 27.37 2.04 54.50 173.04 9.60 11 24D 24D N CA 169 170 173.61 150.30 40.90 12 2304 27T 28E C N 200 202 -73.60 -117.80 58.19 1.79 -63.60 139.62 18.09 12 28E 28E N CA 202 203 98.96 136.80 -40.30 13 2306 29I 30N C N 217 219 -55.49 -71.20 16.28 1.06 -63.20 179.80 22.91 13 30N 30N N CA 219 220 138.54 142.80 -41.10 14 2307 30N 31S C N 225 227 -51.91 -72.40 37.82 1.73 -64.10 156.09 12.08 14 31S 31S N CA 227 228 120.61 152.40 -35.00 15 2308 31S 32T C N 231 233 -128.87 -124.80 4.14 0.20 -63.20 -174.39 28.14 15 32T 32T N CA 233 234 144.29 143.50 -42.10 16 2309 32T 33H C N 238 240 -65.24 -63.20 2.95 0.49 -125.60 -173.21 8.06 16 33H 33H N CA 240 241 -44.43 -42.30 138.80 17 2311 34A 35L C N 253 255 -104.57 -108.50 39.93 2.12 -63.50 140.12 17.57 17 35L 35L N CA 255 256 92.76 132.50 -41.20 18 2320 43A 44P C N 316 318 -68.01 -58.70 13.29 0.93 -64.50 168.24 12.74 18 44P 44P N CA 318 319 -21.01 -30.50 147.20 19 2321 44P 45S C N 323 325 -70.39 -72.40 5.71 0.28 -64.10 178.05 13.28 19 45S 45S N CA 325 326 147.05 152.40 -35.00 20 2328 51A 52G C N 372 374 -92.31 -80.20 17.92 0.54 82.20 -110.15 7.71 20 52G 52G N CA 374 375 -172.69 174.10 8.50 21 2335 58S 59D C N 419 421 52.27 54.50 7.37 0.72 -63.30 137.16 23.38 21 59D 59D N CA 421 422 33.87 40.90 -40.00 22 2337 60R 61A C N 438 440 60.30 -68.20 130.98 11.90 -62.50 -167.35 29.28 22 61A 61A N CA 440 441 170.66 145.30 -40.90 23 2338 61A 62F C N 443 445 -95.51 -71.40 40.56 3.60 -63.20 155.77 19.57 23 62F 62F N CA 445 446 108.08 140.70 -44.30 24 2339 62F 63T C N 454 456 -145.02 -124.80 24.05 0.89 -63.20 -179.07 28.51 24 63T 63T N CA 456 457 156.52 143.50 -42.10 25 2341 64P 65E C N 468 470 69.20 -69.30 138.50 10.48 -63.60 -138.21 25.75 25 65E 65E N CA 470 471 142.06 142.50 -40.30 26 2342 65E 66S C N 477 479 73.48 -72.40 147.18 11.02 -64.10 -154.15 15.92 26 66S 66S N CA 479 480 171.88 152.40 -35.00 27 2344 67V 68M C N 490 492 -95.74 -73.00 36.11 2.83 -63.40 158.78 21.40 27 68M 68M N CA 492 493 114.94 143.00 -40.50 28 2345 68M 69C C N 498 500 -124.22 -117.90 25.89 1.10 -63.00 168.60 17.60 28 69C 69C N CA 500 501 116.00 141.10 -41.10 29 2346 69C 70M C N 504 506 -71.49 -73.00 9.74 0.63 -63.40 174.06 25.37 29 70M 70M N CA 506 507 133.37 143.00 -40.50 30 2347 70M 71H C N 512 514 -82.32 -67.60 53.20 4.49 -63.20 132.56 15.47 30 71H 71H N CA 514 515 88.88 140.00 -42.30 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 8 47 53 60 54 61 59 79 72 << 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 3089.44604 domain0.B99990002.pdb 3122.83154 domain0.B99990003.pdb 3035.10449 domain0.B99990004.pdb 2997.08862 domain0.B99990005.pdb 3024.95166 Dynamically allocated memory at finish [B,KiB,MiB]: 2797039 2731.483 2.667 Starting time : 2019/05/05 16:28:11 Closing time : 2019/05/05 16:28:52 Total CPU time [seconds] : 30.07