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 23:21:15 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_muster10.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 domain1 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]: 396141 386.856 0.378 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 397009 387.704 0.379 Read the alignment from file : bak_muster10.pir Total number of alignment positions: 218 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5CWPA 208 1 MU10A 2 domain1 218 1 check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ./MU10A.atm Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 461134 450.326 0.440 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 461134 450.326 0.440 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 461305 450.493 0.440 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 462155 451.323 0.441 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 463413 452.552 0.442 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 465317 454.411 0.444 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 465317 454.411 0.444 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 465407 454.499 0.444 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 468263 457.288 0.447 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 468263 457.288 0.447 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 468398 457.420 0.447 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 472682 461.604 0.451 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 472682 461.604 0.451 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 472880 461.797 0.451 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 479306 468.072 0.457 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 479306 468.072 0.457 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 479603 468.362 0.457 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489225 477.759 0.467 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 489225 477.759 0.467 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489675 478.198 0.467 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 504125 492.310 0.481 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 504125 492.310 0.481 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 504800 492.969 0.481 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 526458 514.119 0.502 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 526305 513.970 0.502 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]: 665557 649.958 0.635 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 667157 651.521 0.636 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 671137 655.407 0.640 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 673137 657.360 0.642 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 676137 660.290 0.645 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 680637 664.685 0.649 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 686209 670.126 0.654 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 689009 672.860 0.657 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 693209 676.962 0.661 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 699509 683.114 0.667 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 702281 685.821 0.670 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 703681 687.188 0.671 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 737750 720.459 0.704 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 899254 878.178 0.858 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 923222 901.584 0.880 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 218 1629 1662 0 0 667 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 992938 969.666 0.947 patch_______> segment topology patched using RTF: 1 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 1 218 1629 1662 2252 2670 667 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1069714 1044.643 1.020 patch_______> segment topology patched using RTF: 218 ; ALA ; CTER segments residues atoms bonds angles dihedrals impropers: 1 218 1630 1663 2254 2672 668 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 218 1630 1663 2254 2672 668 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 1 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 1542 88 openf___224_> Open domain1.ini wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1176743 1149.163 1.122 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1184935 1157.163 1.130 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1201319 1173.163 1.146 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1234087 1205.163 1.177 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1266855 1237.163 1.208 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1332391 1301.163 1.271 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1365159 1333.163 1.302 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1397927 1365.163 1.333 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1463463 1429.163 1.396 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1594535 1557.163 1.521 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1660071 1621.163 1.583 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 1663 2254 2561 657 Total number of restraints before, now : 0 7135 make_re_422_> Number of previous, current restraints : 0 7135 make_re_423_> Number of previous, current selected restraints: 0 7135 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1782308 1740.535 1.700 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 5CWPA getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 7135 7351 make_re_423_> Number of previous, current selected restraints: 7135 7351 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1782324 1740.551 1.700 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 5CWPA getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 228 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1847860 1804.551 1.762 make_re_422_> Number of previous, current restraints : 7351 7568 make_re_423_> Number of previous, current selected restraints: 7351 7340 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1847860 1804.551 1.762 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 5CWPA getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 7568 7740 make_re_423_> Number of previous, current selected restraints: 7340 7512 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1847860 1804.551 1.762 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 5CWPA getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 7740 7865 make_re_423_> Number of previous, current selected restraints: 7512 7637 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1847860 1804.551 1.762 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 5CWPA getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1978932 1932.551 1.887 make_re_422_> Number of previous, current restraints : 7865 7922 make_re_423_> Number of previous, current selected restraints: 7637 7694 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1978932 1932.551 1.887 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: 5CWPA getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 7922 7943 make_re_423_> Number of previous, current selected restraints: 7694 7715 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 2448336 2390.953 2.335 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2579408 2518.953 2.460 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2841552 2774.953 2.710 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2972624 2902.953 2.835 make_re_422_> Number of previous, current restraints : 7943 12113 make_re_423_> Number of previous, current selected restraints: 7715 11885 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3234768 3158.953 3.085 make_re_422_> Number of previous, current restraints : 12113 16427 make_re_423_> Number of previous, current selected restraints: 11885 16199 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3759056 3670.953 3.585 make_re_422_> Number of previous, current restraints : 16427 19333 make_re_423_> Number of previous, current selected restraints: 16199 19105 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 19333 20861 make_re_423_> Number of previous, current selected restraints: 19105 20633 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 : 20861 20861 make_re_423_> Number of previous, current selected restraints: 20633 20633 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 20861 20861 make_re_423_> Number of previous, current selected restraints: 20633 20633 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 20861 20861 make_re_423_> Number of previous, current selected restraints: 20633 20633 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 20861 20861 make_re_423_> Number of previous, current selected restraints: 20633 20633 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 : 20861 20861 make_re_423_> Number of previous, current selected restraints: 20633 20633 rmdupl__427_> 1302 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 20861 19331 openf___224_> Open domain1.rsr openf___224_> Open domain1.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3897682 3806.330 3.717 rdcsr2__307_> Number of restraints read : 19331 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 19331 19331 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 3897702 3806.350 3.717 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 9996 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11471 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12327 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13301 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14358 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 15190 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16950 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19296 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4229406 4130.279 4.033 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4268526 4168.482 4.071 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 iupac_m_485_> OD1/2 will be swapped: 149.9794 4 4 iupac_m_487_> NH1/2 swapped: 179.4796 22 22 iupac_m_486_> OE1/2 will be swapped: -105.7813 25 25 iupac_m_486_> OE1/2 will be swapped: 98.2748 27 27 iupac_m_483_> CD1/2 CE1/2 swapped: 108.7291 70 70 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_487_> NH1/2 swapped: -178.4053 76 76 iupac_m_483_> CD1/2 CE1/2 swapped: 119.1525 122 122 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: -94.3332 127 127 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_487_> NH1/2 swapped: 177.4359 129 129 iupac_m_483_> CD1/2 CE1/2 swapped: -100.3582 132 132 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: -91.5688 189 189 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 19331 19331 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4620 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 : 2326.0588 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 : 1663 0 0 0.009 0.009 35.566 1.000 2 Bond angle potential : 2254 7 47 3.159 3.159 444.22 1.000 3 Stereochemical cosine torsion poten: 1031 0 25 45.613 45.613 330.62 1.000 4 Stereochemical improper torsion pot: 657 2 5 2.784 2.784 94.086 1.000 5 Soft-sphere overlap restraints : 4620 0 10 0.012 0.012 81.028 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) : 4170 0 16 0.266 0.266 277.08 1.000 10 Distance restraints 2 (N-O) : 4314 1 25 0.325 0.325 325.86 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: 217 4 10 13.329 13.329 127.56 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 8 57.549 57.549 54.257 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 8 64.041 64.041 70.023 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 55.205 55.205 30.431 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 94.892 94.892 15.709 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) : 2906 0 0 0.505 0.505 100.02 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: 216 12 32 27.455 40.537 36.245 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1528 1 32 1.283 1.283 303.34 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 domain1.V99990001 # Heavy relative violation of each residue is written to: domain1.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: 23671.0371 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 2757 110G 111C C N 793 795 144.89 120.00 24.89 5.66 120.00 24.89 5.66 2 2760 111C 111C N CA 795 796 123.80 107.00 16.80 4.83 107.00 16.80 4.83 3 3433 172P 173D C N 1278 1280 145.19 120.00 25.19 5.72 120.00 25.19 5.72 4 3507 179F 179F N CA 1333 1334 126.74 107.00 19.74 5.68 107.00 19.74 5.68 5 3523 180I 180I N CA 1344 1345 139.68 107.00 32.68 9.40 107.00 32.68 9.40 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5832 11T 11T CA C 71 75 -150.52 -180.00 29.48 5.89 -180.00 29.48 5.89 2 6000 179F 179F CA C 1334 1342 -122.94 -180.00 57.06 11.41 -180.00 57.06 11.41 ------------------------------------------------------------------------------------------------- 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 5675 70Y 71A C N 505 507 104.84 55.40 116.81 11.01 -62.50 -117.82 37.27 1 71A 71A N CA 507 508 144.03 38.20 -40.90 2 5676 71A 72I C N 510 512 117.56 -120.60 122.67 8.03 -120.60 122.67 8.03 2 72I 72I N CA 512 513 144.59 130.30 130.30 3 5677 72I 73A C N 518 520 118.26 -134.00 108.15 3.23 -62.50 -117.96 48.62 3 73A 73A N CA 520 521 156.45 147.00 -40.90 4 5678 73A 74H C N 523 525 118.49 56.30 110.88 8.84 56.30 110.88 8.84 4 74H 74H N CA 525 526 -51.00 40.80 40.80 5 5753 148I 149E C N 1082 1084 -67.27 -63.60 47.51 6.54 -63.60 47.51 6.54 5 149E 149E N CA 1084 1085 -87.67 -40.30 -40.30 6 5778 173D 174E C N 1286 1288 -65.71 -69.30 29.83 2.40 -63.60 147.60 19.80 6 174E 174E N CA 1288 1289 172.11 142.50 -40.30 7 5779 174E 175N C N 1295 1297 -135.61 -119.90 40.49 1.44 -63.20 161.71 24.29 7 175N 175N N CA 1297 1298 174.32 137.00 -41.10 8 5780 175N 176D C N 1303 1305 67.24 54.50 39.22 2.03 -63.30 137.69 23.31 8 176D 176D N CA 1305 1306 3.80 40.90 -40.00 9 5781 176D 177Q C N 1311 1313 164.39 -63.80 137.17 20.90 -63.80 137.17 20.90 9 177Q 177Q N CA 1313 1314 -2.31 -40.30 -40.30 10 5782 177Q 178R C N 1320 1322 -157.60 -125.20 71.38 3.93 -63.00 151.31 17.36 10 178R 178R N CA 1322 1323 77.00 140.60 -41.10 11 5783 178R 179F C N 1331 1333 -105.34 -124.20 60.72 3.23 -63.20 122.17 19.75 11 179F 179F N CA 1333 1334 -158.98 143.30 -44.30 12 5785 180I 181V C N 1350 1352 -114.59 -62.40 53.33 7.88 -62.40 53.33 7.88 12 181V 181V N CA 1352 1353 -31.43 -42.40 -42.40 ------------------------------------------------------------------------------------------------- Feature 26 : Distance restraints 4 (SDCH-SDCH) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 18730 122F 203T CE2 CG2 894 1520 9.19 2.70 6.49 4.68 2.70 6.49 4.68 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 7 22 50 146 210 262 242 289 351 351 330 << end of ENERGY. openf___224_> Open domain1.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4268546 4168.502 4.071 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 9996 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11471 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12327 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13301 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14358 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 15190 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16950 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19296 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 iupac_m_485_> OD1/2 will be swapped: 179.5827 3 3 iupac_m_487_> NH1/2 swapped: 178.7438 22 22 iupac_m_486_> OE1/2 will be swapped: -132.0328 40 40 iupac_m_485_> OD1/2 will be swapped: -121.6249 42 42 iupac_m_483_> CD1/2 CE1/2 swapped: 99.3379 70 70 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_487_> NH1/2 swapped: 174.5771 76 76 iupac_m_485_> OD1/2 will be swapped: 154.3928 82 82 iupac_m_486_> OE1/2 will be swapped: -168.9003 90 90 iupac_m_487_> NH1/2 swapped: 179.5130 115 115 iupac_m_483_> CD1/2 CE1/2 swapped: 113.0001 122 122 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: -90.6085 127 127 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_484W> Dihedral still outside +-90: 91.0120 iupac_m_487_> NH1/2 swapped: 172.1971 129 129 iupac_m_486_> OE1/2 will be swapped: -178.0944 171 171 iupac_m_487_> NH1/2 swapped: 165.1503 178 178 iupac_m_486_> OE1/2 will be swapped: -95.3531 205 205 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 19331 19331 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4319 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 : 1845.3457 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 : 1663 0 0 0.008 0.008 29.905 1.000 2 Bond angle potential : 2254 5 35 2.855 2.855 357.97 1.000 3 Stereochemical cosine torsion poten: 1031 0 22 44.799 44.799 326.82 1.000 4 Stereochemical improper torsion pot: 657 2 2 2.078 2.078 53.456 1.000 5 Soft-sphere overlap restraints : 4319 0 0 0.006 0.006 19.064 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) : 4170 0 15 0.238 0.238 216.98 1.000 10 Distance restraints 2 (N-O) : 4314 3 9 0.254 0.254 186.61 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: 217 5 10 13.356 13.356 125.98 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 6 65.812 65.812 59.112 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 3 69.510 69.510 63.945 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 64.025 64.025 34.579 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 1 89.253 89.253 18.567 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) : 2906 0 0 0.493 0.493 93.746 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: 216 10 30 27.775 42.519 15.455 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1528 0 7 1.150 1.150 243.16 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 domain1.V99990002 # Heavy relative violation of each residue is written to: domain1.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: 22854.9082 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 2757 110G 111C C N 793 795 144.83 120.00 24.83 5.64 120.00 24.83 5.64 2 2760 111C 111C N CA 795 796 123.65 107.00 16.65 4.79 107.00 16.65 4.79 3 3412 171E 171E N CA 1264 1265 126.08 107.00 19.08 5.49 107.00 19.08 5.49 4 3424 172P 172P N CA 1273 1274 128.31 108.20 20.12 4.57 108.20 20.12 4.57 5 3523 180I 180I N CA 1344 1345 136.43 107.00 29.43 8.46 107.00 29.43 8.46 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5832 11T 11T CA C 71 75 -148.41 -180.00 31.59 6.32 -180.00 31.59 6.32 2 5992 171E 171E CA C 1265 1271 -155.84 -180.00 24.16 4.83 -180.00 24.16 4.83 3 6000 179F 179F CA C 1334 1342 -135.70 -180.00 44.30 8.86 -180.00 44.30 8.86 4 6001 180I 180I CA C 1345 1350 -137.11 -180.00 42.89 8.58 -180.00 42.89 8.58 ------------------------------------------------------------------------------------------------- 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 5675 70Y 71A C N 505 507 103.16 55.40 118.57 11.00 -62.50 -120.93 36.81 1 71A 71A N CA 507 508 146.73 38.20 -40.90 2 5676 71A 72I C N 510 512 121.24 -120.60 118.60 7.89 -120.60 118.60 7.89 2 72I 72I N CA 512 513 140.57 130.30 130.30 3 5677 72I 73A C N 518 520 117.89 -134.00 110.29 2.90 -62.50 -125.81 47.23 3 73A 73A N CA 520 521 168.82 147.00 -40.90 4 5777 172P 173D C N 1278 1280 -136.34 -96.50 54.15 2.26 -63.30 -175.78 27.46 4 173D 173D N CA 1280 1281 150.88 114.20 -40.00 5 5778 173D 174E C N 1286 1288 -169.72 -117.80 120.69 4.84 -63.60 129.35 22.24 5 174E 174E N CA 1288 1289 -114.25 136.80 -40.30 6 5780 175N 176D C N 1303 1305 165.48 -96.50 98.29 4.01 -63.30 -162.96 21.80 6 176D 176D N CA 1305 1306 106.99 114.20 -40.00 7 5781 176D 177Q C N 1311 1313 150.48 -121.10 100.46 4.78 -63.80 -163.17 25.93 7 177Q 177Q N CA 1313 1314 92.02 139.70 -40.30 8 5782 177Q 178R C N 1320 1322 -55.37 -72.10 16.75 1.26 -63.00 177.85 23.52 8 178R 178R N CA 1322 1323 141.21 141.90 -41.10 9 5783 178R 179F C N 1331 1333 -175.89 -124.20 104.23 3.40 -63.20 139.31 25.14 9 179F 179F N CA 1333 1334 -126.19 143.30 -44.30 10 5784 179F 180I C N 1342 1344 -72.86 -63.40 74.50 12.55 -63.40 74.50 12.55 10 180I 180I N CA 1344 1345 -117.50 -43.60 -43.60 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 24 129 199 225 239 277 356 332 315 << end of ENERGY. openf___224_> Open domain1.B99990002.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4268546 4168.502 4.071 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 9996 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11471 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12327 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13301 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14358 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 15190 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16950 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19296 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 iupac_m_485_> OD1/2 will be swapped: 131.6627 42 42 iupac_m_487_> NH1/2 swapped: -172.5851 59 59 iupac_m_483_> CD1/2 CE1/2 swapped: 101.8671 70 70 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_487_> NH1/2 swapped: 178.3920 76 76 iupac_m_483_> CD1/2 CE1/2 swapped: 91.5154 122 122 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: 135.2505 171 171 iupac_m_485_> OD1/2 will be swapped: 168.2290 176 176 iupac_m_483_> CD1/2 CE1/2 swapped: -96.5922 189 189 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 19331 19331 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4521 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 : 1848.6641 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 : 1663 0 0 0.009 0.009 36.117 1.000 2 Bond angle potential : 2254 7 34 2.922 2.922 383.95 1.000 3 Stereochemical cosine torsion poten: 1031 0 20 44.185 44.185 316.55 1.000 4 Stereochemical improper torsion pot: 657 0 4 1.922 1.922 46.281 1.000 5 Soft-sphere overlap restraints : 4521 1 5 0.010 0.010 49.685 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) : 4170 0 17 0.246 0.246 235.88 1.000 10 Distance restraints 2 (N-O) : 4314 3 8 0.262 0.262 211.52 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: 217 4 8 13.086 13.086 109.29 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 6 57.612 57.612 39.601 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 5 66.583 66.583 70.058 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 69.545 69.545 33.238 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 85.688 85.688 14.753 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) : 2906 0 0 0.454 0.454 76.910 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: 216 11 29 26.302 40.175 12.703 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1528 0 13 1.069 1.069 212.12 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 domain1.V99990003 # Heavy relative violation of each residue is written to: domain1.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: 21601.0996 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 2757 110G 111C C N 793 795 145.55 120.00 25.55 5.81 120.00 25.55 5.81 2 2760 111C 111C N CA 795 796 124.04 107.00 17.04 4.90 107.00 17.04 4.90 3 3484 177Q 177Q CA C 1314 1320 136.30 116.50 19.80 5.69 116.50 19.80 5.69 4 3493 178R 178R N CA 1322 1323 125.51 107.00 18.51 5.32 107.00 18.51 5.32 5 3507 179F 179F N CA 1333 1334 124.72 107.00 17.72 5.10 107.00 17.72 5.10 6 3523 180I 180I N CA 1344 1345 139.41 107.00 32.41 9.32 107.00 32.41 9.32 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5832 11T 11T CA C 71 75 -149.44 -180.00 30.56 6.11 -180.00 30.56 6.11 2 6000 179F 179F CA C 1334 1342 -142.58 -180.00 37.42 7.48 -180.00 37.42 7.48 3 6001 180I 180I CA C 1345 1350 -142.56 -180.00 37.44 7.48 -180.00 37.44 7.48 ------------------------------------------------------------------------------------------------- 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 5675 70Y 71A C N 505 507 102.87 55.40 115.97 10.81 -62.50 -119.15 37.02 1 71A 71A N CA 507 508 144.00 38.20 -40.90 2 5676 71A 72I C N 510 512 118.02 -120.60 122.30 7.98 -120.60 122.30 7.98 2 72I 72I N CA 512 513 145.33 130.30 130.30 3 5677 72I 73A C N 518 520 113.81 -134.00 112.43 3.45 -62.50 -118.62 37.59 3 73A 73A N CA 520 521 154.23 147.00 -40.90 4 5678 73A 74H C N 523 525 125.51 56.30 114.21 9.54 56.30 114.21 9.54 4 74H 74H N CA 525 526 -50.05 40.80 40.80 5 5777 172P 173D C N 1278 1280 -104.24 -63.30 43.94 7.47 -63.30 43.94 7.47 5 173D 173D N CA 1280 1281 -55.96 -40.00 -40.00 6 5778 173D 174E C N 1286 1288 -175.43 -117.80 60.56 1.84 -63.60 -161.25 32.57 6 174E 174E N CA 1288 1289 155.40 136.80 -40.30 7 5779 174E 175N C N 1295 1297 -107.34 -119.90 63.37 3.14 -63.20 127.67 18.47 7 175N 175N N CA 1297 1298 -160.89 137.00 -41.10 8 5781 176D 177Q C N 1311 1313 -106.13 -121.10 33.14 1.73 -63.80 156.28 25.24 8 177Q 177Q N CA 1313 1314 169.26 139.70 -40.30 9 5782 177Q 178R C N 1320 1322 -147.02 -125.20 32.85 1.03 -63.00 175.20 29.34 9 178R 178R N CA 1322 1323 165.16 140.60 -41.10 10 5783 178R 179F C N 1331 1333 -144.16 -124.20 105.13 4.42 -63.20 106.50 19.17 10 179F 179F N CA 1333 1334 -113.48 143.30 -44.30 11 5784 179F 180I C N 1342 1344 -92.47 -63.40 76.42 13.59 -63.40 76.42 13.59 11 180I 180I N CA 1344 1345 -114.28 -43.60 -43.60 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 1 5 21 36 152 201 259 233 298 340 354 306 << end of ENERGY. openf___224_> Open domain1.B99990003.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4268546 4168.502 4.071 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 9996 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11471 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12327 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13301 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14358 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 15190 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16950 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19296 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 iupac_m_485_> OD1/2 will be swapped: -174.6599 4 4 iupac_m_486_> OE1/2 will be swapped: -162.1775 27 27 iupac_m_485_> OD1/2 will be swapped: 117.8041 56 56 iupac_m_483_> CD1/2 CE1/2 swapped: 101.9626 70 70 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_487_> NH1/2 swapped: 178.9624 76 76 iupac_m_486_> OE1/2 will be swapped: 150.7161 121 121 iupac_m_483_> CD1/2 CE1/2 swapped: 119.1387 122 122 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: -100.4859 127 127 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 107.6269 135 135 iupac_m_486_> OE1/2 will be swapped: -119.0913 171 171 iupac_m_485_> OD1/2 will be swapped: 138.8373 173 173 iupac_m_487_> NH1/2 swapped: 172.0929 178 178 iupac_m_483_> CD1/2 CE1/2 swapped: 98.2748 179 179 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 132.0978 182 182 iupac_m_487_> NH1/2 swapped: -178.9560 211 211 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 19331 19331 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4539 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 : 2047.2354 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 : 1663 0 1 0.008 0.008 31.729 1.000 2 Bond angle potential : 2254 4 30 2.844 2.844 348.93 1.000 3 Stereochemical cosine torsion poten: 1031 0 25 44.738 44.738 320.00 1.000 4 Stereochemical improper torsion pot: 657 0 4 1.876 1.876 46.309 1.000 5 Soft-sphere overlap restraints : 4539 0 4 0.009 0.009 42.257 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) : 4170 0 1 0.249 0.249 224.11 1.000 10 Distance restraints 2 (N-O) : 4314 3 11 0.316 0.316 289.15 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: 217 1 11 12.603 12.603 78.363 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 9 61.203 61.203 64.384 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 5 66.822 66.822 65.317 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 60.835 60.835 34.328 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 103.066 103.066 15.239 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) : 2906 0 0 0.498 0.498 99.695 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: 216 17 31 30.787 47.293 128.03 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1528 0 14 1.209 1.209 259.40 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 domain1.V99990004 # Heavy relative violation of each residue is written to: domain1.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: 23573.8848 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 2757 110G 111C C N 793 795 145.29 120.00 25.29 5.75 120.00 25.29 5.75 2 2760 111C 111C N CA 795 796 123.91 107.00 16.91 4.86 107.00 16.91 4.86 3 3412 171E 171E N CA 1264 1265 124.74 107.00 17.74 5.10 107.00 17.74 5.10 4 3520 179F 180I C N 1342 1344 140.19 120.00 20.19 4.59 120.00 20.19 4.59 ------------------------------------------------------------------------------------------------- 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 5615 10L 11T C N 68 70 -47.91 -63.20 65.36 7.47 -63.20 65.36 7.47 1 11T 11T N CA 70 71 -105.64 -42.10 -42.10 2 5616 11T 12P C N 75 77 -162.61 -58.70 105.54 12.42 -64.50 -172.97 19.09 2 12P 12P N CA 77 78 -12.03 -30.50 147.20 3 5646 41V 42D C N 300 302 51.73 54.50 70.89 4.99 -63.30 -169.59 30.72 3 42D 42D N CA 302 303 111.73 40.90 -40.00 4 5675 70Y 71A C N 505 507 105.77 -134.00 120.23 3.97 -62.50 -119.57 37.09 4 71A 71A N CA 507 508 147.37 147.00 -40.90 5 5676 71A 72I C N 510 512 116.60 -120.60 123.75 8.07 -120.60 123.75 8.07 5 72I 72I N CA 512 513 145.59 130.30 130.30 6 5677 72I 73A C N 518 520 111.25 -134.00 114.94 3.56 -62.50 -119.96 37.30 6 73A 73A N CA 520 521 153.48 147.00 -40.90 7 5678 73A 74H C N 523 525 125.06 56.30 111.79 9.43 56.30 111.79 9.43 7 74H 74H N CA 525 526 -47.34 40.80 40.80 8 5723 118V 119T C N 865 867 -61.43 -63.20 142.98 18.45 -63.20 142.98 18.45 8 119T 119T N CA 867 868 100.87 -42.10 -42.10 9 5724 119T 120G C N 872 874 -61.39 -62.40 35.40 5.34 82.20 144.30 10.17 9 120G 120G N CA 874 875 -5.81 -41.20 8.50 10 5777 172P 173D C N 1278 1280 16.30 -70.90 95.01 7.95 -63.30 154.12 16.38 10 173D 173D N CA 1280 1281 -171.97 150.30 -40.00 11 5778 173D 174E C N 1286 1288 -68.55 -69.30 27.17 2.10 -63.60 150.12 20.29 11 174E 174E N CA 1288 1289 169.66 142.50 -40.30 12 5779 174E 175N C N 1295 1297 -151.22 -119.90 40.93 1.19 -63.20 178.73 27.26 12 175N 175N N CA 1297 1298 163.35 137.00 -41.10 13 5780 175N 176D C N 1303 1305 -132.36 -96.50 83.21 3.45 -63.30 105.02 11.58 13 176D 176D N CA 1305 1306 39.12 114.20 -40.00 14 5781 176D 177Q C N 1311 1313 -174.72 -121.10 117.47 6.13 -63.80 134.18 18.34 14 177Q 177Q N CA 1313 1314 35.19 139.70 -40.30 15 5782 177Q 178R C N 1320 1322 -50.49 -72.10 22.22 1.58 -63.00 178.28 24.93 15 178R 178R N CA 1322 1323 136.74 141.90 -41.10 16 5783 178R 179F C N 1331 1333 -146.07 -63.20 83.02 13.10 -63.20 83.02 13.10 16 179F 179F N CA 1333 1334 -39.45 -44.30 -44.30 17 5784 179F 180I C N 1342 1344 -73.93 -63.40 99.92 16.02 -63.40 99.92 16.02 17 180I 180I N CA 1344 1345 55.76 -43.60 -43.60 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 6 19 42 178 204 253 228 302 373 327 306 << end of ENERGY. openf___224_> Open domain1.B99990004.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4268546 4168.502 4.071 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 9996 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11471 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12327 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13301 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14358 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 15190 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16950 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19296 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 19331 iupac_m_486_> OE1/2 will be swapped: -170.9029 40 40 iupac_m_485_> OD1/2 will be swapped: 94.1940 42 42 iupac_m_485_> OD1/2 will be swapped: 144.0159 51 51 iupac_m_487_> NH1/2 swapped: -176.0870 53 53 iupac_m_483_> CD1/2 CE1/2 swapped: 100.1562 70 70 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: 114.5454 86 86 iupac_m_487_> NH1/2 swapped: 179.6774 115 115 iupac_m_486_> OE1/2 will be swapped: 131.3536 121 121 iupac_m_486_> OE1/2 will be swapped: -168.1251 131 131 iupac_m_486_> OE1/2 will be swapped: 153.0407 149 149 iupac_m_486_> OE1/2 will be swapped: -175.0518 157 157 iupac_m_485_> OD1/2 will be swapped: -92.9685 173 173 iupac_m_485_> OD1/2 will be swapped: 172.0785 176 176 iupac_m_487_> NH1/2 swapped: -170.5145 178 178 iupac_m_483_> CD1/2 CE1/2 swapped: -91.9855 189 189 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: 94.2663 196 196 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_484W> Dihedral still outside +-90: -90.1152 iupac_m_487_> NH1/2 swapped: 179.4770 211 211 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 19331 19331 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4531 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 : 1711.7692 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 : 1663 0 1 0.009 0.009 38.386 1.000 2 Bond angle potential : 2254 3 35 2.932 2.932 372.56 1.000 3 Stereochemical cosine torsion poten: 1031 0 23 44.884 44.884 323.27 1.000 4 Stereochemical improper torsion pot: 657 0 3 1.896 1.896 47.094 1.000 5 Soft-sphere overlap restraints : 4531 0 3 0.009 0.009 46.930 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) : 4170 0 1 0.205 0.205 168.37 1.000 10 Distance restraints 2 (N-O) : 4314 0 10 0.270 0.270 214.49 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: 217 2 9 12.477 12.477 72.567 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 2 51.883 51.883 23.632 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 7 68.272 68.272 65.731 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 57.878 57.878 31.659 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 85.700 85.700 15.769 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) : 2906 0 0 0.430 0.430 72.275 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: 216 12 32 29.230 43.453 24.254 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1528 0 5 1.029 1.029 194.78 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 domain1.V99990005 # Heavy relative violation of each residue is written to: domain1.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: 21561.1328 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 2757 110G 111C C N 793 795 145.41 120.00 25.41 5.77 120.00 25.41 5.77 2 2760 111C 111C N CA 795 796 124.02 107.00 17.02 4.89 107.00 17.02 4.89 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5832 11T 11T CA C 71 75 -149.25 -180.00 30.75 6.15 -180.00 30.75 6.15 ------------------------------------------------------------------------------------------------- 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 5675 70Y 71A C N 505 507 105.34 55.40 116.49 11.03 -62.50 -117.05 37.38 1 71A 71A N CA 507 508 143.44 38.20 -40.90 2 5676 71A 72I C N 510 512 123.93 -120.60 115.99 7.69 -120.60 115.99 7.69 2 72I 72I N CA 512 513 141.29 130.30 130.30 3 5677 72I 73A C N 518 520 110.09 -134.00 116.10 3.60 -62.50 -120.84 37.14 3 73A 73A N CA 520 521 153.53 147.00 -40.90 4 5678 73A 74H C N 523 525 125.05 56.30 112.72 9.46 56.30 112.72 9.46 4 74H 74H N CA 525 526 -48.53 40.80 40.80 5 5777 172P 173D C N 1278 1280 178.38 -70.90 124.49 6.87 -63.30 163.46 27.29 5 173D 173D N CA 1280 1281 -152.79 150.30 -40.00 6 5778 173D 174E C N 1286 1288 153.90 -117.80 99.76 4.83 -63.60 -166.65 23.34 6 174E 174E N CA 1288 1289 90.37 136.80 -40.30 7 5779 174E 175N C N 1295 1297 -102.72 -119.90 28.64 1.55 -63.20 163.83 22.73 7 175N 175N N CA 1297 1298 159.91 137.00 -41.10 8 5780 175N 176D C N 1303 1305 -16.05 54.50 78.30 6.85 -63.30 124.20 18.39 8 176D 176D N CA 1305 1306 74.86 40.90 -40.00 9 5781 176D 177Q C N 1311 1313 142.35 -63.80 153.85 25.69 -63.80 153.85 25.69 9 177Q 177Q N CA 1313 1314 -41.31 -40.30 -40.30 10 5782 177Q 178R C N 1320 1322 -148.13 -125.20 23.04 0.87 -63.00 -164.50 32.21 10 178R 178R N CA 1322 1323 142.91 140.60 -41.10 11 5783 178R 179F C N 1331 1333 -52.90 -71.40 51.79 4.55 -63.20 127.04 16.96 11 179F 179F N CA 1333 1334 -170.93 140.70 -44.30 12 5784 179F 180I C N 1342 1344 -70.96 -63.40 44.07 7.50 -63.40 44.07 7.50 12 180I 180I N CA 1344 1345 -87.02 -43.60 -43.60 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 2 17 34 164 228 264 227 302 369 348 308 << end of ENERGY. openf___224_> Open domain1.B99990005.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 >> Summary of successfully produced models: Filename molpdf ---------------------------------------- domain1.B99990001.pdb 2326.05884 domain1.B99990002.pdb 1845.34570 domain1.B99990003.pdb 1848.66406 domain1.B99990004.pdb 2047.23535 domain1.B99990005.pdb 1711.76917 Dynamically allocated memory at finish [B,KiB,MiB]: 4268526 4168.482 4.071 Starting time : 2019/05/05 23:21:15 Closing time : 2019/05/05 23:22:33 Total CPU time [seconds] : 78.15