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): 2019/05/07 07:27:05 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_deepcomb5.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]: 275589 269.130 0.263 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 278629 272.099 0.266 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 395313 386.048 0.377 check_prot_W> Alignment sequence deepcomb5 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]: 395673 386.399 0.377 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 396541 387.247 0.378 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 397753 388.431 0.379 Read the alignment from file : bak_deepcomb5.pir Total number of alignment positions: 304 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 meta_com1 91 1 meta_com1_d 2 meta_hhsu 218 1 meta_hhsu3_ 3 deepcomb5 304 1 check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ./meta_com1_dom0.atm Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 426778 416.775 0.407 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 426778 416.775 0.407 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 426949 416.942 0.407 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 427799 417.772 0.408 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 429057 419.001 0.409 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 430961 420.860 0.411 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 430961 420.860 0.411 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 431051 420.948 0.411 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 433907 423.737 0.414 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 433907 423.737 0.414 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 434042 423.869 0.414 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 438326 428.053 0.418 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 438326 428.053 0.418 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 438524 428.246 0.418 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 444950 434.521 0.424 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 444950 434.521 0.424 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 445247 434.812 0.425 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 454869 444.208 0.434 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 454788 444.129 0.434 openf___224_> Open ./meta_hhsu3_dom1.atm Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 521913 509.681 0.498 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 521913 509.681 0.498 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 522084 509.848 0.498 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 522934 510.678 0.499 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 524192 511.906 0.500 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 526096 513.766 0.502 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 526096 513.766 0.502 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 526186 513.854 0.502 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 529042 516.643 0.505 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 529042 516.643 0.505 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 529177 516.774 0.505 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 533461 520.958 0.509 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 533461 520.958 0.509 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 533659 521.151 0.509 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 540085 527.427 0.515 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 540085 527.427 0.515 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 540382 527.717 0.515 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 550004 537.113 0.525 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 550004 537.113 0.525 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 550454 537.553 0.525 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 564904 551.664 0.539 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 564904 551.664 0.539 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 565579 552.323 0.539 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 587237 573.474 0.560 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 587174 573.412 0.560 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 ---------------------------------------------- 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]: 726426 709.400 0.693 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 728026 710.963 0.694 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 732006 714.850 0.698 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 734006 716.803 0.700 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 737006 719.732 0.703 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 741506 724.127 0.707 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 747078 729.568 0.712 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 749878 732.303 0.715 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 754078 736.404 0.719 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 760378 742.557 0.725 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 763150 745.264 0.728 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 764550 746.631 0.729 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 812121 793.087 0.774 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1035659 1011.386 0.988 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1068891 1043.839 1.019 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 304 2262 2306 0 0 924 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1165791 1138.468 1.112 patch_______> segment topology patched using RTF: 1 ; THR ; NTER segments residues atoms bonds angles dihedrals impropers: 1 304 2262 2306 3128 3712 924 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1276287 1246.374 1.217 patch_______> segment topology patched using RTF: 304 ; ALA ; CTER segments residues atoms bonds angles dihedrals impropers: 1 304 2263 2307 3130 3714 925 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 304 2263 2307 3130 3714 925 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 2 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 2263 0 openf___224_> Open deepcomb5.ini wrpdb___568_> Residues, atoms, selected atoms: 304 2263 2263 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1383316 1350.895 1.319 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1391508 1358.895 1.327 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1407892 1374.895 1.343 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1440660 1406.895 1.374 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1473428 1438.895 1.405 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1538964 1502.895 1.468 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1571732 1534.895 1.499 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1604500 1566.895 1.530 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1670036 1630.895 1.593 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1801108 1758.895 1.718 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1866644 1822.895 1.780 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1932180 1886.895 1.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2063252 2014.895 1.968 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2325396 2270.895 2.218 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 2307 3130 3557 909 Total number of restraints before, now : 0 9903 make_re_422_> Number of previous, current restraints : 0 9903 make_re_423_> Number of previous, current selected restraints: 0 9903 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2495729 2437.235 2.380 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: meta_com1 getdata_643_> Protein accepted: meta_hhsu3 getdata_289_> Proteins (all/accepted): 2 2 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2626837 2565.271 2.505 make_re_422_> Number of previous, current restraints : 9903 10205 make_re_423_> Number of previous, current selected restraints: 9903 10205 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2626837 2565.271 2.505 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: meta_com1 getdata_643_> Protein accepted: meta_hhsu3 getdata_289_> Proteins (all/accepted): 2 2 omgdel__425_> Unselected all O C +N +CA dihedrals: 319 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 10205 10508 make_re_423_> Number of previous, current selected restraints: 10205 10189 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2626837 2565.271 2.505 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: meta_com1 getdata_643_> Protein accepted: meta_hhsu3 getdata_289_> Proteins (all/accepted): 2 2 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2757909 2693.271 2.630 make_re_422_> Number of previous, current restraints : 10508 10752 make_re_423_> Number of previous, current selected restraints: 10189 10433 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2757909 2693.271 2.630 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: meta_com1 getdata_643_> Protein accepted: meta_hhsu3 getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 10752 10922 make_re_423_> Number of previous, current selected restraints: 10433 10603 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2757909 2693.271 2.630 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: meta_com1 getdata_643_> Protein accepted: meta_hhsu3 getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 10922 11000 make_re_423_> Number of previous, current selected restraints: 10603 10681 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2757909 2693.271 2.630 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: meta_com1 getdata_643_> Protein accepted: meta_hhsu3 getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 11000 11028 make_re_423_> Number of previous, current selected restraints: 10681 10709 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 3409617 3329.704 3.252 make_re_422_> Number of previous, current restraints : 11028 16067 make_re_423_> Number of previous, current selected restraints: 10709 15748 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3671761 3585.704 3.502 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4196049 4097.704 4.002 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4458193 4353.704 4.252 make_re_422_> Number of previous, current restraints : 16067 21150 make_re_423_> Number of previous, current selected restraints: 15748 20831 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4720337 4609.704 4.502 make_re_422_> Number of previous, current restraints : 21150 26266 make_re_423_> Number of previous, current selected restraints: 20831 25947 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 26266 28503 make_re_423_> Number of previous, current selected restraints: 25947 28184 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 : 28503 28503 make_re_423_> Number of previous, current selected restraints: 28184 28184 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 28503 28503 make_re_423_> Number of previous, current selected restraints: 28184 28184 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 28503 28503 make_re_423_> Number of previous, current selected restraints: 28184 28184 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 28503 28503 make_re_423_> Number of previous, current selected restraints: 28184 28184 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 : 28503 28503 make_re_423_> Number of previous, current selected restraints: 28184 28184 rmdupl__427_> 1818 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 28503 26366 openf___224_> Open deepcomb5.rsr openf___224_> Open deepcomb5.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4749978 4638.650 4.530 rdcsr2__307_> Number of restraints read : 26366 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 26366 26366 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 openf___224_> Open deepcomb5.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4749998 4638.670 4.530 read_mo_297_> Segments, residues, atoms: 1 304 2263 read_mo_298_> Segment: 1 1 304 2263 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2263 2263 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2263 15179 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 16889 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 17751 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 18713 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 19979 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 20519 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 21931 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 23125 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 24535 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 5096894 4977.436 4.861 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26308 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26366 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26366 iupac_m_487_> NH1/2 swapped: 176.0311 2 2 iupac_m_487_> NH1/2 swapped: 178.9188 16 16 iupac_m_486_> OE1/2 will be swapped: 162.5654 20 20 iupac_m_487_> NH1/2 swapped: 177.2688 21 21 iupac_m_486_> OE1/2 will be swapped: 91.7430 28 28 iupac_m_487_> NH1/2 swapped: -178.0774 60 60 iupac_m_485_> OD1/2 will be swapped: 130.3329 89 89 iupac_m_487_> NH1/2 swapped: 179.0276 108 108 iupac_m_487_> NH1/2 swapped: -176.6046 162 162 iupac_m_487_> NH1/2 swapped: 178.2173 201 201 iupac_m_485_> OD1/2 will be swapped: -106.1642 221 221 iupac_m_486_> OE1/2 will be swapped: 123.5929 243 243 iupac_m_483_> CD1/2 CE1/2 swapped: -93.3551 247 247 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: 92.8835 282 282 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: -130.4061 291 291 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 304 Number of all, selected real atoms : 2263 2263 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 26366 26366 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4418 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 : 1427.5035 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 : 2307 0 0 0.004 0.004 9.4986 1.000 2 Bond angle potential : 3130 0 1 1.767 1.767 190.28 1.000 3 Stereochemical cosine torsion poten: 1420 0 43 49.434 49.434 545.70 1.000 4 Stereochemical improper torsion pot: 909 0 0 1.051 1.051 20.677 1.000 5 Soft-sphere overlap restraints : 4418 0 0 0.002 0.002 1.4780 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) : 5039 0 0 0.126 0.126 64.901 1.000 10 Distance restraints 2 (N-O) : 5083 0 1 0.156 0.156 77.823 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: 303 0 2 3.638 3.638 47.297 1.000 14 Sidechain Chi_1 dihedral restraints: 244 0 0 55.288 55.288 13.849 1.000 15 Sidechain Chi_2 dihedral restraints: 170 0 1 56.084 56.084 43.337 1.000 16 Sidechain Chi_3 dihedral restraints: 78 0 0 59.513 59.513 42.737 1.000 17 Sidechain Chi_4 dihedral restraints: 28 0 0 101.106 101.106 24.501 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) : 5116 0 0 0.402 0.402 230.79 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: 302 3 13 23.878 29.594 -15.810 1.000 26 Distance restraints 4 (SDCH-SDCH) : 2237 0 5 0.629 0.629 130.44 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 deepcomb5.V99990001 # Heavy relative violation of each residue is written to: deepcomb5.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: 20463.7715 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 7767 1T 2R C N 6 8 -61.01 -63.00 3.29 0.38 -72.10 174.74 13.68 1 2R 2R N CA 8 9 -43.72 -41.10 141.90 2 7829 63T 64P C N 461 463 -67.89 -58.70 27.61 3.04 -64.50 156.30 11.49 2 64P 64P N CA 463 464 -56.53 -30.50 147.20 3 7958 192A 193D C N 1398 1400 85.42 -70.90 173.22 14.53 -70.90 173.22 14.53 3 193D 193D N CA 1400 1401 -135.07 150.30 150.30 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 9 35 95 129 196 207 271 311 328 329 << end of ENERGY. openf___224_> Open deepcomb5.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 304 2263 2263 openf___224_> Open deepcomb5.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5096914 4977.455 4.861 read_mo_297_> Segments, residues, atoms: 1 304 2263 read_mo_298_> Segment: 1 1 304 2263 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2263 2263 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2263 15179 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 16889 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 17751 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 18713 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 19979 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 20519 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 21931 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 23125 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 24535 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26308 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26366 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26366 iupac_m_487_> NH1/2 swapped: -179.4415 2 2 iupac_m_487_> NH1/2 swapped: -176.7588 42 42 iupac_m_485_> OD1/2 will be swapped: -145.1363 100 100 iupac_m_487_> NH1/2 swapped: 177.5329 108 108 iupac_m_486_> OE1/2 will be swapped: -167.2324 113 113 iupac_m_485_> OD1/2 will be swapped: 145.4723 123 123 iupac_m_485_> OD1/2 will be swapped: 142.1656 193 193 iupac_m_486_> OE1/2 will be swapped: 165.7833 229 229 iupac_m_487_> NH1/2 swapped: 177.1154 297 297 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 304 Number of all, selected real atoms : 2263 2263 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 26366 26366 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4446 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 : 1399.9346 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 : 2307 0 0 0.004 0.004 9.0651 1.000 2 Bond angle potential : 3130 0 2 1.740 1.740 184.66 1.000 3 Stereochemical cosine torsion poten: 1420 0 35 48.328 48.328 520.53 1.000 4 Stereochemical improper torsion pot: 909 0 0 0.943 0.943 16.939 1.000 5 Soft-sphere overlap restraints : 4446 0 0 0.001 0.001 1.0882 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) : 5039 0 1 0.116 0.116 58.759 1.000 10 Distance restraints 2 (N-O) : 5083 2 8 0.152 0.152 109.56 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: 303 0 1 3.373 3.373 40.644 1.000 14 Sidechain Chi_1 dihedral restraints: 244 0 0 56.832 56.832 14.388 1.000 15 Sidechain Chi_2 dihedral restraints: 170 0 0 56.782 56.782 43.702 1.000 16 Sidechain Chi_3 dihedral restraints: 78 0 0 57.746 57.746 40.146 1.000 17 Sidechain Chi_4 dihedral restraints: 28 0 0 93.610 93.610 19.772 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) : 5116 0 0 0.384 0.384 232.16 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: 302 4 13 25.715 31.570 -3.4184 1.000 26 Distance restraints 4 (SDCH-SDCH) : 2237 0 0 0.585 0.585 111.94 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 deepcomb5.V99990002 # Heavy relative violation of each residue is written to: deepcomb5.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: 20001.4648 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 15840 160H 214P N O 1158 1575 9.78 7.46 2.32 4.59 7.46 2.32 4.59 2 15865 161N 214P N O 1168 1575 10.73 8.29 2.44 4.68 8.29 2.44 4.68 ------------------------------------------------------------------------------------------------- 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 7822 56A 57P C N 406 408 -67.39 -58.70 8.83 1.20 -64.50 179.29 13.53 1 57P 57P N CA 408 409 -32.06 -30.50 147.20 2 7958 192A 193D C N 1398 1400 85.55 -70.90 173.86 14.58 -70.90 173.86 14.58 2 193D 193D N CA 1400 1401 -133.87 150.30 150.30 3 7979 213Y 214P C N 1567 1569 -72.00 -58.70 23.55 1.43 -64.50 158.44 12.22 3 214P 214P N CA 1569 1570 -11.07 -30.50 147.20 4 7980 214P 215R C N 1574 1576 70.89 -72.10 144.36 10.58 -72.10 144.36 10.58 4 215R 215R N CA 1576 1577 122.06 141.90 141.90 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 34 105 147 191 211 246 315 324 347 << end of ENERGY. openf___224_> Open deepcomb5.B99990002.pdb wrpdb___568_> Residues, atoms, selected atoms: 304 2263 2263 openf___224_> Open deepcomb5.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5096914 4977.455 4.861 read_mo_297_> Segments, residues, atoms: 1 304 2263 read_mo_298_> Segment: 1 1 304 2263 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2263 2263 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2263 15179 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 16889 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 17751 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 18713 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 19979 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 20519 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 21931 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 23125 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 24535 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26308 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26366 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26366 iupac_m_487_> NH1/2 swapped: 178.8802 2 2 iupac_m_486_> OE1/2 will be swapped: 177.9838 20 20 iupac_m_487_> NH1/2 swapped: -179.9802 21 21 iupac_m_487_> NH1/2 swapped: 179.7925 26 26 iupac_m_487_> NH1/2 swapped: -179.6004 60 60 iupac_m_486_> OE1/2 will be swapped: 177.0772 126 126 iupac_m_487_> NH1/2 swapped: -174.6879 139 139 iupac_m_485_> OD1/2 will be swapped: 140.3483 193 193 iupac_m_487_> NH1/2 swapped: 179.7459 201 201 iupac_m_486_> OE1/2 will be swapped: 149.2598 217 217 iupac_m_485_> OD1/2 will be swapped: 121.2467 221 221 iupac_m_487_> NH1/2 swapped: -173.5824 297 297 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 304 Number of all, selected real atoms : 2263 2263 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 26366 26366 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4471 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 : 1333.7849 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 : 2307 0 0 0.004 0.004 8.4514 1.000 2 Bond angle potential : 3130 0 0 1.717 1.717 180.05 1.000 3 Stereochemical cosine torsion poten: 1420 0 41 49.187 49.187 535.37 1.000 4 Stereochemical improper torsion pot: 909 0 0 0.935 0.935 16.960 1.000 5 Soft-sphere overlap restraints : 4471 0 0 0.001 0.001 0.59328 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) : 5039 0 0 0.103 0.103 51.411 1.000 10 Distance restraints 2 (N-O) : 5083 0 2 0.135 0.135 80.054 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: 303 0 2 3.516 3.516 44.181 1.000 14 Sidechain Chi_1 dihedral restraints: 244 0 0 56.022 56.022 15.548 1.000 15 Sidechain Chi_2 dihedral restraints: 170 0 0 56.269 56.269 41.932 1.000 16 Sidechain Chi_3 dihedral restraints: 78 0 0 63.088 63.088 40.321 1.000 17 Sidechain Chi_4 dihedral restraints: 28 0 0 87.731 87.731 16.648 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) : 5116 0 0 0.375 0.375 223.63 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: 302 3 10 25.120 28.325 -20.975 1.000 26 Distance restraints 4 (SDCH-SDCH) : 2237 0 0 0.550 0.550 99.620 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 deepcomb5.V99990003 # Heavy relative violation of each residue is written to: deepcomb5.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: 19895.1387 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 7886 120I 121S C N 879 881 62.47 -64.10 154.35 14.44 -72.40 159.02 12.79 1 121S 121S N CA 881 882 -123.34 -35.00 152.40 2 7887 121S 122Q C N 885 887 -66.41 -63.80 13.54 1.86 55.10 138.91 18.49 2 122Q 122Q N CA 887 888 -27.02 -40.30 40.30 3 7958 192A 193D C N 1398 1400 87.50 -70.90 175.73 14.74 -70.90 175.73 14.74 3 193D 193D N CA 1400 1401 -133.61 150.30 150.30 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 11 28 90 149 176 221 261 298 335 352 << end of ENERGY. openf___224_> Open deepcomb5.B99990003.pdb wrpdb___568_> Residues, atoms, selected atoms: 304 2263 2263 openf___224_> Open deepcomb5.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5096914 4977.455 4.861 read_mo_297_> Segments, residues, atoms: 1 304 2263 read_mo_298_> Segment: 1 1 304 2263 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2263 2263 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2263 15179 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 16889 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 17751 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 18713 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 19979 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 20519 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 21931 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 23125 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 24535 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26308 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26366 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26366 iupac_m_487_> NH1/2 swapped: 178.2149 2 2 iupac_m_487_> NH1/2 swapped: -177.8431 16 16 iupac_m_487_> NH1/2 swapped: -179.8082 21 21 iupac_m_486_> OE1/2 will be swapped: 115.0848 46 46 iupac_m_487_> NH1/2 swapped: -175.4833 60 60 iupac_m_486_> OE1/2 will be swapped: -119.1868 65 65 iupac_m_485_> OD1/2 will be swapped: 154.0850 89 89 iupac_m_485_> OD1/2 will be swapped: 145.6603 90 90 iupac_m_486_> OE1/2 will be swapped: -150.9079 111 111 iupac_m_485_> OD1/2 will be swapped: 165.2031 128 128 iupac_m_487_> NH1/2 swapped: 178.4999 145 145 iupac_m_487_> NH1/2 swapped: 178.5878 162 162 iupac_m_485_> OD1/2 will be swapped: -95.6293 221 221 iupac_m_486_> OE1/2 will be swapped: -115.3456 260 260 iupac_m_487_> NH1/2 swapped: 179.8864 297 297 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 304 Number of all, selected real atoms : 2263 2263 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 26366 26366 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4507 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 : 1373.3481 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 : 2307 0 0 0.004 0.004 9.3906 1.000 2 Bond angle potential : 3130 0 1 1.758 1.758 187.29 1.000 3 Stereochemical cosine torsion poten: 1420 0 37 47.965 47.965 512.53 1.000 4 Stereochemical improper torsion pot: 909 0 0 0.972 0.972 18.062 1.000 5 Soft-sphere overlap restraints : 4507 0 0 0.001 0.001 1.1612 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) : 5039 0 4 0.128 0.128 69.430 1.000 10 Distance restraints 2 (N-O) : 5083 0 3 0.155 0.155 95.962 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: 303 0 1 3.521 3.521 44.300 1.000 14 Sidechain Chi_1 dihedral restraints: 244 0 0 54.951 54.951 7.2034 1.000 15 Sidechain Chi_2 dihedral restraints: 170 0 2 56.904 56.904 46.696 1.000 16 Sidechain Chi_3 dihedral restraints: 78 0 2 61.285 61.285 45.148 1.000 17 Sidechain Chi_4 dihedral restraints: 28 0 0 103.231 103.231 18.114 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) : 5116 0 0 0.395 0.395 237.80 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: 302 4 12 23.869 30.031 -23.766 1.000 26 Distance restraints 4 (SDCH-SDCH) : 2237 0 0 0.561 0.561 104.03 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 deepcomb5.V99990004 # Heavy relative violation of each residue is written to: deepcomb5.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: 20261.2207 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 7790 24D 25P C N 175 177 -76.12 -58.70 20.87 1.79 -64.50 166.61 13.06 1 25P 25P N CA 177 178 -19.01 -30.50 147.20 2 7886 120I 121S C N 879 881 62.35 -64.10 153.19 14.43 -72.40 159.92 12.87 2 121S 121S N CA 881 882 -121.47 -35.00 152.40 3 7887 121S 122Q C N 885 887 -65.07 -63.80 12.44 1.76 55.10 138.19 18.39 3 122Q 122Q N CA 887 888 -27.93 -40.30 40.30 4 7958 192A 193D C N 1398 1400 84.31 -63.30 173.42 21.79 -70.90 174.01 14.60 4 193D 193D N CA 1400 1401 -131.02 -40.00 150.30 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 10 26 83 143 175 216 285 319 330 345 << end of ENERGY. openf___224_> Open deepcomb5.B99990004.pdb wrpdb___568_> Residues, atoms, selected atoms: 304 2263 2263 openf___224_> Open deepcomb5.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5096914 4977.455 4.861 read_mo_297_> Segments, residues, atoms: 1 304 2263 read_mo_298_> Segment: 1 1 304 2263 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2263 2263 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2263 15179 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 16889 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 17751 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 18713 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 19979 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 20519 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 21931 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 23125 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 24535 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26308 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26366 pick_re_612_> Number of MODEL atoms, selected restraints; 2263 26366 iupac_m_487_> NH1/2 swapped: 179.4482 26 26 iupac_m_487_> NH1/2 swapped: -177.0958 42 42 iupac_m_485_> OD1/2 will be swapped: -143.2262 73 73 iupac_m_485_> OD1/2 will be swapped: -151.0125 90 90 iupac_m_487_> NH1/2 swapped: 175.3313 108 108 iupac_m_483_> CD1/2 CE1/2 swapped: -106.6393 199 199 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -108.7853 200 200 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: -156.5723 217 217 iupac_m_485_> OD1/2 will be swapped: 111.8576 221 221 iupac_m_486_> OE1/2 will be swapped: 153.1568 235 235 iupac_m_486_> OE1/2 will be swapped: 104.2630 243 243 iupac_m_486_> OE1/2 will be swapped: 175.0096 260 260 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 304 Number of all, selected real atoms : 2263 2263 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 26366 26366 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4437 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 : 1329.5546 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 : 2307 0 0 0.004 0.004 9.3517 1.000 2 Bond angle potential : 3130 0 1 1.691 1.691 173.89 1.000 3 Stereochemical cosine torsion poten: 1420 0 37 48.851 48.851 533.43 1.000 4 Stereochemical improper torsion pot: 909 0 0 0.941 0.941 16.921 1.000 5 Soft-sphere overlap restraints : 4437 0 0 0.001 0.001 0.92183 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) : 5039 0 0 0.110 0.110 54.593 1.000 10 Distance restraints 2 (N-O) : 5083 0 0 0.125 0.125 64.733 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: 303 0 2 3.410 3.410 41.547 1.000 14 Sidechain Chi_1 dihedral restraints: 244 0 1 54.591 54.591 12.425 1.000 15 Sidechain Chi_2 dihedral restraints: 170 0 0 56.054 56.054 44.816 1.000 16 Sidechain Chi_3 dihedral restraints: 78 0 0 58.381 58.381 41.623 1.000 17 Sidechain Chi_4 dihedral restraints: 28 0 0 103.624 103.624 19.886 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) : 5116 0 0 0.374 0.374 220.77 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: 302 4 10 24.266 30.495 -16.037 1.000 26 Distance restraints 4 (SDCH-SDCH) : 2237 0 0 0.579 0.579 110.68 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 deepcomb5.V99990005 # Heavy relative violation of each residue is written to: deepcomb5.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: 19881.3418 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 7770 4G 5C C N 27 29 -59.90 -63.00 17.47 1.94 -117.90 170.76 7.41 1 5C 5C N CA 29 30 -58.29 -41.10 141.10 2 7822 56A 57P C N 406 408 -52.11 -58.70 37.38 2.59 -64.50 146.04 11.56 2 57P 57P N CA 408 409 -67.29 -30.50 147.20 3 7856 90D 91T C N 661 663 -75.17 -63.20 12.88 2.20 -124.80 176.77 9.02 3 91T 91T N CA 663 664 -46.84 -42.10 143.50 4 7958 192A 193D C N 1398 1400 85.49 -70.90 173.31 14.54 -70.90 173.31 14.54 4 193D 193D N CA 1400 1401 -135.00 150.30 150.30 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 11 25 91 163 169 215 255 303 327 326 << end of ENERGY. openf___224_> Open deepcomb5.B99990005.pdb wrpdb___568_> Residues, atoms, selected atoms: 304 2263 2263 >> Summary of successfully produced models: Filename molpdf ---------------------------------------- deepcomb5.B99990001.pdb 1427.50354 deepcomb5.B99990002.pdb 1399.93457 deepcomb5.B99990003.pdb 1333.78491 deepcomb5.B99990004.pdb 1373.34814 deepcomb5.B99990005.pdb 1329.55457 Dynamically allocated memory at finish [B,KiB,MiB]: 5096894 4977.436 4.861 Starting time : 2019/05/07 07:27:05 Closing time : 2019/05/07 07:28:09 Total CPU time [seconds] : 63.80