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 22:41:30 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-multiple.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]: 331397 323.630 0.316 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 331609 323.837 0.316 Read the alignment from file : align-multiple.ali Total number of alignment positions: 106 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 106 1 5fd1 ferredoxin 2 1bqx 77 1 1bqx ferredoxin 3 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]: 365134 356.576 0.348 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 365134 356.576 0.348 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 365305 356.743 0.348 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 366155 357.573 0.349 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 367413 358.802 0.350 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 369317 360.661 0.352 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 369317 360.661 0.352 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 369407 360.749 0.352 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 372263 363.538 0.355 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 372263 363.538 0.355 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 372398 363.670 0.355 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 376682 367.854 0.359 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 376682 367.854 0.359 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 376880 368.047 0.359 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383306 374.322 0.366 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 383306 374.322 0.366 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383603 374.612 0.366 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 393225 384.009 0.375 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 393225 384.009 0.375 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 393675 384.448 0.375 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 393279 384.062 0.375 openf___224_> Open ../atom_files/pdb1bqx.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 418104 408.305 0.399 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 418104 408.305 0.399 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 418275 408.472 0.399 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 419125 409.302 0.400 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 420383 410.530 0.401 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 422287 412.390 0.403 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 422287 412.390 0.403 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 422377 412.478 0.403 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 425233 415.267 0.406 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 425233 415.267 0.406 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 425368 415.398 0.406 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 429652 419.582 0.410 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 429652 419.582 0.410 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 429850 419.775 0.410 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 436276 426.051 0.416 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 436276 426.051 0.416 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 436573 426.341 0.416 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 446195 435.737 0.426 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 445988 435.535 0.425 check_ali___> Checking pairwise structural superpositions. Equivalent CA pairs with distance difference larger than 6.0 angstroms: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- END OF TABLE check_ali___> Checking the sequence-structure alignment. Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- 8 2 8 11 C I 9.338 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]: 585240 571.523 0.558 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 586840 573.086 0.560 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 590820 576.973 0.563 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 592820 578.926 0.565 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 595820 581.855 0.568 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 600320 586.250 0.573 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 605892 591.691 0.578 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 608692 594.426 0.580 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 612892 598.527 0.584 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 619192 604.680 0.591 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 621964 607.387 0.593 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 623364 608.754 0.594 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 631685 616.880 0.602 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 670003 654.300 0.639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 675427 659.597 0.644 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]: 691663 675.452 0.660 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]: 709639 693.007 0.677 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 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 2 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 340 33 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]: 816668 797.527 0.779 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 824860 805.527 0.787 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 841244 821.527 0.802 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 874012 853.527 0.834 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]: 902835 881.675 0.861 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 5fd1 getdata_643_> Protein accepted: 1bqx getdata_289_> Proteins (all/accepted): 2 2 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]: 902871 881.710 0.861 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 5fd1 getdata_643_> Protein accepted: 1bqx getdata_289_> Proteins (all/accepted): 2 2 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]: 902871 881.710 0.861 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 5fd1 getdata_643_> Protein accepted: 1bqx getdata_289_> Proteins (all/accepted): 2 2 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]: 902871 881.710 0.861 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 5fd1 getdata_643_> Protein accepted: 1bqx getdata_289_> Proteins (all/accepted): 2 2 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]: 902871 881.710 0.861 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 5fd1 getdata_643_> Protein accepted: 1bqx getdata_289_> Proteins (all/accepted): 2 2 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]: 902871 881.710 0.861 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_643_> Protein accepted: 1bqx getdata_289_> Proteins (all/accepted): 2 2 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]: 1010259 986.581 0.963 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1043027 1018.581 0.995 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1075795 1050.581 1.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1141331 1114.581 1.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1206867 1178.581 1.151 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1337939 1306.581 1.276 make_re_422_> Number of previous, current restraints : 1845 2678 make_re_423_> Number of previous, current selected restraints: 1787 2620 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1370707 1338.581 1.307 make_re_422_> Number of previous, current restraints : 2678 3598 make_re_423_> Number of previous, current selected restraints: 2620 3540 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1632851 1594.581 1.557 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1698387 1658.581 1.620 make_re_422_> Number of previous, current restraints : 3598 4312 make_re_423_> Number of previous, current selected restraints: 3540 4254 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4312 4488 make_re_423_> Number of previous, current selected restraints: 4254 4430 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 : 4488 4488 make_re_423_> Number of previous, current selected restraints: 4430 4430 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4488 4488 make_re_423_> Number of previous, current selected restraints: 4430 4430 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4488 4488 make_re_423_> Number of previous, current selected restraints: 4430 4430 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4488 4488 make_re_423_> Number of previous, current selected restraints: 4430 4430 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 : 4488 4488 make_re_423_> Number of previous, current selected restraints: 4430 4430 rmdupl__427_> 314 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 4488 4116 openf___224_> Open 1fdx.rsr openf___224_> Open 1fdx.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1551972 1515.598 1.480 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1650276 1611.598 1.574 rdcsr2__307_> Number of restraints read : 4116 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 4116 4116 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]: 1650296 1611.617 1.574 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 2382 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2652 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2829 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2997 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3417 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1951832 1906.086 1.861 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3698 pick_re_612_> Number of MODEL atoms, selected restraints; 373 4094 pick_re_612_> Number of MODEL atoms, selected restraints; 373 4116 iupac_m_485_> OD1/2 will be swapped: 152.1875 54 54 >> 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 : 4116 4116 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 603 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 : 1788.9330 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 0.005 0.005 2.9340 1.000 2 Bond angle potential : 520 0 3 2.371 2.371 55.760 1.000 3 Stereochemical cosine torsion poten: 244 0 7 51.340 51.340 94.972 1.000 4 Stereochemical improper torsion pot: 146 0 0 1.119 1.119 4.3810 1.000 5 Soft-sphere overlap restraints : 603 0 0 0.002 0.002 0.26829 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) : 833 8 2 0.721 0.721 380.10 1.000 10 Distance restraints 2 (N-O) : 920 16 8 0.875 0.875 505.91 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 1 5.254 5.254 17.256 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 0 78.479 78.479 10.766 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 0 58.255 58.255 8.9609 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 0 46.879 46.879 3.3756 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 88.527 88.527 1.2205 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) : 714 0 0 0.595 0.595 536.36 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 9 34.634 70.290 42.835 1.000 26 Distance restraints 4 (SDCH-SDCH) : 176 0 1 0.953 0.953 123.83 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: 6550.3062 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 10 : Distance restraints 2 (N-O) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 2405 5N 49A N O 33 333 4.31 2.74 1.57 5.17 2.74 1.57 5.17 2 2704 24Q 14C N O 164 94 8.79 6.01 2.77 4.90 6.01 2.77 4.90 3 2719 25G 14C N O 173 94 11.24 7.94 3.30 4.90 7.94 3.30 4.90 4 2764 28Y 14C N O 191 94 9.82 6.76 3.07 5.63 6.76 3.07 5.63 5 2784 29A 14C N O 203 94 9.75 6.75 3.01 5.51 6.75 3.01 5.51 6 2801 30I 14C N O 208 94 9.83 7.45 2.38 5.80 7.45 2.38 5.80 ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1293 4I 5N C N 31 33 -116.73 -119.90 41.47 1.96 -63.20 150.40 21.85 1 5N 5N N CA 33 34 178.35 137.00 -41.10 2 1296 7S 8C C N 53 55 -86.11 -117.90 35.08 0.98 -63.00 168.95 19.15 2 8C 8C N CA 55 56 126.26 141.10 -41.10 3 1297 8C 9I C N 59 61 -103.09 -97.30 5.97 0.30 -63.40 176.77 27.72 3 9I 9I N CA 61 62 128.65 127.20 -43.60 4 1298 9I 10A C N 67 69 -58.96 -68.20 16.14 1.57 -62.50 160.60 26.15 4 10A 10A N CA 69 70 158.54 145.30 -40.90 5 1310 21N 22I C N 146 148 -113.39 -120.60 75.28 4.02 -63.40 110.88 16.91 5 22I 22I N CA 148 149 55.37 130.30 -43.60 6 1313 24Q 25G C N 171 173 128.34 78.70 58.76 1.85 -80.20 151.91 10.45 6 25G 25G N CA 173 174 162.45 -166.10 174.10 7 1327 38C 39G C N 269 271 -147.09 -62.40 110.53 15.95 -62.40 110.53 15.95 7 39G 39G N CA 271 272 29.83 -41.20 -41.20 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 1 2 18 20 32 29 30 36 46 49 << 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 1788.93298 Dynamically allocated memory at finish [B,KiB,MiB]: 1951832 1906.086 1.861 Starting time : 2016/04/05 22:41:30 Closing time : 2016/04/05 22:41:34 Total CPU time [seconds] : 3.03