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 22:41:07 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 alignment.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]: 331093 323.333 0.316 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 331305 323.540 0.316 Read the alignment from file : alignment.ali Total number of alignment positions: 106 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 106 1 5fd1 ferredoxin 2 1fdx 54 1 1fdx ferredoxin check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ../atom_files/pdb5fd1.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 364830 356.279 0.348 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 364830 356.279 0.348 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 365001 356.446 0.348 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 365851 357.276 0.349 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 367109 358.505 0.350 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 369013 360.364 0.352 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 369013 360.364 0.352 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 369103 360.452 0.352 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 371959 363.241 0.355 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 371959 363.241 0.355 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 372094 363.373 0.355 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 376378 367.557 0.359 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 376378 367.557 0.359 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 376576 367.750 0.359 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383002 374.025 0.365 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 383002 374.025 0.365 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383299 374.315 0.366 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 392921 383.712 0.375 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 392921 383.712 0.375 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 393371 384.151 0.375 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 392975 383.765 0.375 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]: 532227 519.753 0.508 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 533827 521.315 0.509 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 537807 525.202 0.513 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 539807 527.155 0.515 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 542807 530.085 0.518 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 547307 534.479 0.522 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 552879 539.921 0.527 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 555679 542.655 0.530 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 559879 546.757 0.534 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 566179 552.909 0.540 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 568951 555.616 0.543 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 570351 556.983 0.544 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 578672 565.109 0.552 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 616990 602.529 0.588 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 622414 607.826 0.594 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 54 372 378 0 0 150 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 638650 623.682 0.609 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 54 372 378 518 628 150 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 656626 641.236 0.626 patch_______> segment topology patched using RTF: 54 ; ASP ; CTER segments residues atoms bonds angles dihedrals impropers: 1 54 373 379 520 630 151 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 54 373 379 520 630 151 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 660490 645.010 0.630 patch_______> segment topology patched using RTF: 8 45 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 54 373 380 522 633 151 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: 322 51 openf___224_> Open 1fdx.ini wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 767519 749.530 0.732 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 775711 757.530 0.740 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 792095 773.530 0.755 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 824863 805.530 0.787 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 380 522 621 146 Total number of restraints before, now : 0 1669 make_re_422_> Number of previous, current restraints : 0 1669 make_re_423_> Number of previous, current selected restraints: 0 1669 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 853686 833.678 0.814 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 1669 1721 make_re_423_> Number of previous, current selected restraints: 1669 1721 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 853702 833.693 0.814 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 : 1721 1774 make_re_423_> Number of previous, current selected restraints: 1721 1716 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 853702 833.693 0.814 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 : 1774 1817 make_re_423_> Number of previous, current selected restraints: 1716 1759 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 853702 833.693 0.814 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 : 1817 1843 make_re_423_> Number of previous, current selected restraints: 1759 1785 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 853702 833.693 0.814 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 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 886470 865.693 0.845 make_re_422_> Number of previous, current restraints : 1843 1852 make_re_423_> Number of previous, current selected restraints: 1785 1794 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 886470 865.693 0.845 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 make_re_422_> Number of previous, current restraints : 1852 1853 make_re_423_> Number of previous, current selected restraints: 1794 1795 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 993858 970.564 0.948 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1026626 1002.564 0.979 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1092162 1066.564 1.042 make_re_422_> Number of previous, current restraints : 1853 2657 make_re_423_> Number of previous, current selected restraints: 1795 2599 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1124930 1098.564 1.073 make_re_422_> Number of previous, current restraints : 2657 3494 make_re_423_> Number of previous, current selected restraints: 2599 3436 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 3494 4047 make_re_423_> Number of previous, current selected restraints: 3436 3989 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1190466 1162.564 1.135 make_re_422_> Number of previous, current restraints : 4047 4147 make_re_423_> Number of previous, current selected restraints: 3989 4089 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 : 4147 4147 make_re_423_> Number of previous, current selected restraints: 4089 4089 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4147 4147 make_re_423_> Number of previous, current selected restraints: 4089 4089 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4147 4147 make_re_423_> Number of previous, current selected restraints: 4089 4089 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4147 4147 make_re_423_> Number of previous, current selected restraints: 4089 4089 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 : 4147 4147 make_re_423_> Number of previous, current selected restraints: 4089 4089 rmdupl__427_> 316 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 4147 3773 openf___224_> Open 1fdx.rsr openf___224_> Open 1fdx.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1097084 1071.371 1.046 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1195388 1167.371 1.140 rdcsr2__307_> Number of restraints read : 3773 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 3773 3773 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 openf___224_> Open 1fdx.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1195408 1167.391 1.140 read_mo_297_> Segments, residues, atoms: 1 54 373 read_mo_298_> Segment: 1 1 54 373 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 373 373 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 373 2207 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2464 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2618 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2758 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3111 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1496944 1461.859 1.428 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3372 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3752 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3773 iupac_m_485_> OD1/2 will be swapped: -176.4798 6 6 iupac_m_483_> CD1/2 CE1/2 swapped: -97.3515 28 28 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: 136.0882 33 33 iupac_m_485_> OD1/2 will be swapped: -140.1820 37 37 iupac_m_486_> OE1/2 will be swapped: -134.5536 53 53 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 373 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 3773 3773 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 660 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 : 308.1328 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 0.006 0.006 3.8829 1.000 2 Bond angle potential : 520 0 0 2.370 2.370 57.390 1.000 3 Stereochemical cosine torsion poten: 246 0 9 54.388 54.388 100.22 1.000 4 Stereochemical improper torsion pot: 146 0 0 1.393 1.393 5.6015 1.000 5 Soft-sphere overlap restraints : 660 0 0 0.002 0.002 0.39297 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 1 0.408 0.408 36.625 1.000 10 Distance restraints 2 (N-O) : 837 0 0 0.469 0.469 35.720 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 4.540 4.540 12.883 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 0 68.348 68.348 8.1191 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 0 69.040 69.040 10.108 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 0 67.590 67.590 4.0446 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 2.447 2.447 0.24105 1.000 18 Disulfide distance restraints : 1 0 0 0.028 0.028 0.13683 1.000 19 Disulfide angle restraints : 2 0 0 5.611 5.611 1.3903 1.000 20 Disulfide dihedral angle restraints: 1 0 0 24.666 24.666 0.65187 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 0.503 0.503 13.950 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 7 4 21.444 60.185 5.3301 1.000 26 Distance restraints 4 (SDCH-SDCH) : 100 0 0 1.198 1.198 11.450 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 1fdx.V99990001 # Heavy relative violation of each residue is written to: 1fdx.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: 5130.0405 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 1302 7S 8C C N 53 55 -78.08 -117.90 42.44 1.22 -63.00 168.18 19.53 1 8C 8C N CA 55 56 126.40 141.10 -41.10 2 1303 8C 9I C N 59 61 -101.80 -97.30 51.31 5.30 -63.40 125.70 19.47 2 9I 9I N CA 61 62 76.09 127.20 -43.60 3 1304 9I 10A C N 67 69 48.64 55.40 16.88 0.61 -62.50 145.92 29.41 3 10A 10A N CA 69 70 53.66 38.20 -40.90 4 1305 10A 11C C N 72 74 -65.49 -63.00 5.10 0.81 -117.90 -178.90 7.78 4 11C 11C N CA 74 75 -45.55 -41.10 141.10 5 1316 21N 22I C N 146 148 -107.20 -120.60 72.38 3.63 -63.40 111.72 17.12 5 22I 22I N CA 148 149 59.18 130.30 -43.60 6 1319 24Q 25G C N 171 173 103.41 78.70 44.87 0.72 82.20 149.46 8.31 6 25G 25G N CA 173 174 156.45 -166.10 8.50 7 1320 25G 26S C N 175 177 -66.72 -64.10 12.98 1.12 -136.60 175.59 9.89 7 26S 26S N CA 177 178 -47.71 -35.00 151.20 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 5 3 15 26 33 28 45 44 64 43 << end of ENERGY. openf___224_> Open 1fdx.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 >> Summary of successfully produced models: Filename molpdf ---------------------------------------- 1fdx.B99990001.pdb 308.13284 Dynamically allocated memory at finish [B,KiB,MiB]: 1496944 1461.859 1.428 Starting time : 2016/04/05 22:41:07 Closing time : 2016/04/05 22:41:09 Total CPU time [seconds] : 2.41