MODELLER 9.16, 2016/01/07, r10745 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2016 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux sunflower.rnet.missouri.edu 2.6.32-431.23.3.el6.x86_64 x86_64 Date and time of compilation : 2016/01/07 10:19:44 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2016/04/05 22:41:09 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 align-ligand.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 265439 259.218 0.253 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 266889 260.634 0.255 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269789 263.466 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 330673 322.923 0.315 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 331101 323.341 0.316 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 331321 323.556 0.316 read_al_374_> Non-standard residue type,position,sequence: . 107 1 read_al_374_> Non-standard residue type,position,sequence: . 108 1 read_al_374_> Non-standard residue type,position,sequence: . 107 2 read_al_374_> Non-standard residue type,position,sequence: . 108 2 Read the alignment from file : align-ligand.ali Total number of alignment positions: 108 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 108 1 5fd1 ferredoxin 2 1fdx 56 1 1fdx ferredoxin check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ../atom_files/pdb5fd1.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 365446 356.881 0.349 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 365446 356.881 0.349 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 365617 357.048 0.349 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 366467 357.878 0.349 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 367725 359.106 0.351 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 369629 360.966 0.353 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 369629 360.966 0.353 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 369719 361.054 0.353 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 372575 363.843 0.355 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 372575 363.843 0.355 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 372710 363.975 0.355 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 376994 368.158 0.360 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 376994 368.158 0.360 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 377192 368.352 0.360 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383618 374.627 0.366 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 383618 374.627 0.366 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383915 374.917 0.366 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 393537 384.313 0.375 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 393537 384.313 0.375 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 393987 384.753 0.376 read_pd_459W> Residue type SF4 not recognized. 'automodel' model building will treat this residue as a rigid body. To use real parameters, add the residue type to ${LIB}/restyp.lib, its topology to ${LIB}/top_*.lib, and suitable forcefield parameters to ${LIB}/par.lib. Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 408437 398.864 0.390 rdpdb___459W> Residue type F3S not recognized. 'automodel' model building will treat this residue as a rigid body. To use real parameters, add the residue type to ${LIB}/restyp.lib, its topology to ${LIB}/top_*.lib, and suitable forcefield parameters to ${LIB}/par.lib. Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 408059 398.495 0.389 fndatmi_285W> Only 106 residues out of 108 contain atoms of type CA (This is usually caused by non-standard residues, such as ligands, or by PDB files with missing atoms.) fndatmi_285W> Only 106 residues out of 108 contain atoms of type CA (This is usually caused by non-standard residues, such as ligands, or by PDB files with missing atoms.) 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]: 547311 534.483 0.522 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 548911 536.046 0.523 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 552891 539.933 0.527 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 554891 541.886 0.529 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 557891 544.815 0.532 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 562391 549.210 0.536 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 567963 554.651 0.542 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 570763 557.386 0.544 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 574963 561.487 0.548 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 581263 567.640 0.554 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 584035 570.347 0.557 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 585435 571.714 0.558 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 594070 580.146 0.567 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 632388 617.566 0.603 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 637812 622.863 0.608 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 3 54 atom names : C +N atom indices : 371 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 3 54 atom names : C CA +N O atom indices : 371 366 0 372 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 56 387 378 0 0 150 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 654048 638.719 0.624 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 56 387 378 518 628 150 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 672024 656.273 0.641 patch_______> segment topology patched using RTF: 54 ; ASP ; CTER segments residues atoms bonds angles dihedrals impropers: 1 56 388 379 520 630 151 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 56 388 379 520 630 151 fndatmi_285W> Only 106 residues out of 108 contain atoms of type CA (This is usually caused by non-standard residues, such as ligands, or by PDB files with missing atoms.) 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: 337 51 openf___224_> Open 1fdx.ini wrpdb___568_> Residues, atoms, selected atoms: 56 388 388 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 779053 760.794 0.743 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 787245 768.794 0.751 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 803629 784.794 0.766 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 836397 816.794 0.798 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 379 520 616 146 Total number of restraints before, now : 0 1661 make_re_422_> Number of previous, current restraints : 0 1661 make_re_423_> Number of previous, current selected restraints: 0 1661 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 866348 846.043 0.826 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 105 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 106 ARG errdih__638_> Missing atoms in a dihedral, residue index, residue type: 3 106 ARG errdih__638_> Missing atoms in a dihedral, residue index, residue type: 4 106 ARG getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 1661 1713 make_re_423_> Number of previous, current selected restraints: 1661 1713 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 866364 846.059 0.826 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 58 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 1713 1766 make_re_423_> Number of previous, current selected restraints: 1713 1708 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 866364 846.059 0.826 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 1766 1809 make_re_423_> Number of previous, current selected restraints: 1708 1751 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 866364 846.059 0.826 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 1809 1835 make_re_423_> Number of previous, current selected restraints: 1751 1777 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 866364 846.059 0.826 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 1835 1844 make_re_423_> Number of previous, current selected restraints: 1777 1786 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 866364 846.059 0.826 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: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 899132 878.059 0.857 make_re_422_> Number of previous, current restraints : 1844 1845 make_re_423_> Number of previous, current selected restraints: 1786 1787 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1010840 987.148 0.964 iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: FE1 --> C This message is written only for the first such atom. Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1043608 1019.148 0.995 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1109144 1083.148 1.058 make_re_422_> Number of previous, current restraints : 1845 2649 make_re_423_> Number of previous, current selected restraints: 1787 2591 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1141912 1115.148 1.089 make_re_422_> Number of previous, current restraints : 2649 3486 make_re_423_> Number of previous, current selected restraints: 2591 3428 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 3486 4039 make_re_423_> Number of previous, current selected restraints: 3428 3981 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1207448 1179.148 1.152 make_re_422_> Number of previous, current restraints : 4039 4139 make_re_423_> Number of previous, current selected restraints: 3981 4081 15 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 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1207600 1179.297 1.152 make_re_422_> Number of previous, current restraints : 4139 4143 make_re_423_> Number of previous, current selected restraints: 4081 4085 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4143 4526 make_re_423_> Number of previous, current selected restraints: 4085 4468 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4526 4526 make_re_423_> Number of previous, current selected restraints: 4468 4468 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4526 4526 make_re_423_> Number of previous, current selected restraints: 4468 4468 15 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 : 4526 4624 make_re_423_> Number of previous, current selected restraints: 4468 4566 rmdupl__427_> 314 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 4624 4252 openf___224_> Open 1fdx.rsr openf___224_> Open 1fdx.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1098006 1072.271 1.047 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1196310 1168.271 1.141 rdcsr2__307_> Number of restraints read : 4252 Number of excluded pairs read: 4 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 4252 4252 Explicitly excluded atom pairs in memory : 4 Pseudo atoms in memory : 0 openf___224_> Open 1fdx.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1196330 1168.291 1.141 read_mo_297_> Segments, residues, atoms: 1 56 388 read_mo_298_> Segment: 1 1 56 388 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 388 373 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 388 2301 pick_re_612_> Number of MODEL atoms, selected restraints; 388 2567 pick_re_612_> Number of MODEL atoms, selected restraints; 388 2734 pick_re_612_> Number of MODEL atoms, selected restraints; 388 2901 pick_re_612_> Number of MODEL atoms, selected restraints; 388 3351 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1498226 1463.111 1.429 pick_re_612_> Number of MODEL atoms, selected restraints; 388 3665 pick_re_612_> Number of MODEL atoms, selected restraints; 388 4195 pick_re_612_> Number of MODEL atoms, selected restraints; 388 4252 iupac_m_485_> OD1/2 will be swapped: 162.0685 6 6 iupac_m_485_> OD1/2 will be swapped: 93.4424 37 37 iupac_m_485_> OD1/2 will be swapped: 174.3925 54 54 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 56 Number of all, selected real atoms : 388 388 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 4252 4252 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 742 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 : 333.2075 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 : 379 0 0 0.007 0.007 5.1715 1.000 2 Bond angle potential : 520 0 2 2.593 2.593 68.550 1.000 3 Stereochemical cosine torsion poten: 244 0 12 55.858 55.858 103.43 1.000 4 Stereochemical improper torsion pot: 146 0 0 1.352 1.352 5.5836 1.000 5 Soft-sphere overlap restraints : 742 0 0 0.003 0.003 0.71816 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) : 804 0 0 0.213 0.213 9.7421 1.000 10 Distance restraints 2 (N-O) : 837 0 0 0.408 0.408 32.561 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: 53 0 0 5.333 5.333 17.773 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 0 67.779 67.779 12.322 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 0 75.349 75.349 11.592 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 0 63.700 63.700 2.8078 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 117.819 117.819 0.95162 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) : 553 0 0 0.504 0.504 13.613 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: 52 6 7 31.349 62.893 25.091 1.000 26 Distance restraints 4 (SDCH-SDCH) : 100 0 0 0.888 0.888 6.9339 1.000 27 Distance restraints 5 (X-Y) : 485 0 1 0.067 0.067 16.362 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 1fdx.V99990004 # Heavy relative violation of each residue is written to: 1fdx.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: 5185.4360 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 1296 7S 8C C N 53 55 -57.33 -117.90 64.19 1.86 -63.00 161.05 20.04 1 8C 8C N CA 55 56 119.85 141.10 -41.10 2 1297 8C 9I C N 59 61 -107.04 -97.30 88.79 9.15 -63.40 93.38 14.23 2 9I 9I N CA 61 62 38.95 127.20 -43.60 3 1298 9I 10A C N 67 69 42.99 55.40 30.23 1.09 -62.50 150.02 29.95 3 10A 10A N CA 69 70 65.77 38.20 -40.90 4 1299 10A 11C C N 72 74 -67.76 -63.00 6.15 1.08 -117.90 -179.02 7.75 4 11C 11C N CA 74 75 -45.01 -41.10 141.10 5 1310 21N 22I C N 146 148 -107.06 -120.60 74.39 3.74 -63.40 109.81 16.82 5 22I 22I N CA 148 149 57.15 130.30 -43.60 6 1313 24Q 25G C N 171 173 -81.49 -80.20 4.76 0.13 82.20 -123.88 7.23 6 25G 25G N CA 173 174 178.68 174.10 8.50 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 4 2 22 19 40 34 35 61 55 60 << end of ENERGY. openf___224_> Open 1fdx.B99990004.pdb wrpdb___568_> Residues, atoms, selected atoms: 56 388 388 >> Summary of successfully produced models: Filename molpdf ---------------------------------------- 1fdx.B99990004.pdb 333.20749 Dynamically allocated memory at finish [B,KiB,MiB]: 1498226 1463.111 1.429 Starting time : 2016/04/05 22:41:09 Closing time : 2016/04/05 22:41:12 Total CPU time [seconds] : 2.62