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 22:38:15 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 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]: 299873 292.845 0.286 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 300089 293.056 0.286 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 300305 293.267 0.286 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 300517 293.474 0.287 Read the alignment from file : alignment.ali Total number of alignment positions: 56 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1durA 55 1 1dur MOL_ID 1; MOLECULE 2[4FE-4S] FERREDOXIN; CHAIN A 2 2fdnA 55 1 2fdn MOL_ID 1; MOLECULE FERREDOXIN; CHAIN A 3 1fdx_my 54 1 1fdx ferredoxin check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ../atom_files/pdb1dur.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 318742 311.271 0.304 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 318742 311.271 0.304 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 318913 311.438 0.304 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 319763 312.269 0.305 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 321021 313.497 0.306 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 322925 315.356 0.308 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 322925 315.356 0.308 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 323015 315.444 0.308 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 325871 318.233 0.311 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 325871 318.233 0.311 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 326006 318.365 0.311 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 330290 322.549 0.315 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 330290 322.549 0.315 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 330488 322.742 0.315 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 336914 329.018 0.321 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 336806 328.912 0.321 Uncompressing compressed file with system command: gzip -d -c ../atom_files/pdb2fdn.ent.gz > /tmp/pdb2fdn.ent.W2MTFY openf___224_> Open ../atom_files/pdb2fdn.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 355031 346.710 0.339 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 355031 346.710 0.339 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 355202 346.877 0.339 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 356052 347.707 0.340 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 357310 348.936 0.341 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 359214 350.795 0.343 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 359214 350.795 0.343 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 359304 350.883 0.343 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 362160 353.672 0.345 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 362160 353.672 0.345 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 362295 353.804 0.346 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 366579 357.987 0.350 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 366579 357.987 0.350 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 366777 358.181 0.350 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 373203 364.456 0.356 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 373095 364.351 0.356 check_ali___> Checking pairwise structural superpositions. Equivalent CA pairs with distance difference larger than 6.0 angstroms: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- END OF TABLE check_ali___> Checking the sequence-structure alignment. Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE check_a_344_> << END OF COMMAND openf___224_> Open ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 512347 500.339 0.489 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 513947 501.901 0.490 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 517927 505.788 0.494 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 519927 507.741 0.496 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 522927 510.671 0.499 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 527427 515.065 0.503 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 532999 520.507 0.508 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 535799 523.241 0.511 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 539999 527.343 0.515 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 546299 533.495 0.521 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 549071 536.202 0.524 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 550471 537.569 0.525 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 558792 545.695 0.533 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 597110 583.115 0.569 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 602534 588.412 0.575 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]: 618770 604.268 0.590 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]: 636746 621.822 0.607 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: 368 5 openf___224_> Open 1fdx_my.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]: 743775 726.343 0.709 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 751967 734.343 0.717 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 768351 750.343 0.733 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 801119 782.343 0.764 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]: 829942 810.490 0.791 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: 5 27 SER getdata_643_> Protein accepted: 1durA getdata_643_> Protein accepted: 2fdnA 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]: 829978 810.525 0.792 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 1durA getdata_643_> Protein accepted: 2fdnA 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]: 829978 810.525 0.792 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 1durA getdata_643_> Protein accepted: 2fdnA 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]: 829978 810.525 0.792 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 1durA getdata_643_> Protein accepted: 2fdnA 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]: 829978 810.525 0.792 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 1durA getdata_643_> Protein accepted: 2fdnA 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]: 829978 810.525 0.792 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: 1durA getdata_643_> Protein accepted: 2fdnA 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]: 937366 915.396 0.894 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 970134 947.396 0.925 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1002902 979.396 0.956 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1068438 1043.396 1.019 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1133974 1107.396 1.081 make_re_422_> Number of previous, current restraints : 1845 2668 make_re_423_> Number of previous, current selected restraints: 1787 2610 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1166742 1139.396 1.113 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1297814 1267.396 1.238 make_re_422_> Number of previous, current restraints : 2668 3573 make_re_423_> Number of previous, current selected restraints: 2610 3515 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1559958 1523.396 1.488 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1625494 1587.396 1.550 make_re_422_> Number of previous, current restraints : 3573 4425 make_re_423_> Number of previous, current selected restraints: 3515 4367 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1756566 1715.396 1.675 make_re_422_> Number of previous, current restraints : 4425 4699 make_re_423_> Number of previous, current selected restraints: 4367 4641 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 : 4699 4699 make_re_423_> Number of previous, current selected restraints: 4641 4641 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4699 4699 make_re_423_> Number of previous, current selected restraints: 4641 4641 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4699 4699 make_re_423_> Number of previous, current selected restraints: 4641 4641 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4699 4699 make_re_423_> Number of previous, current selected restraints: 4641 4641 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 : 4699 4699 make_re_423_> Number of previous, current selected restraints: 4641 4641 rmdupl__427_> 314 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 4699 4327 openf___224_> Open 1fdx_my.rsr openf___224_> Open 1fdx_my.rsr rdcsr2__307_> Number of restraints read : 4327 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 4327 4327 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 openf___224_> Open 1fdx_my.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1617528 1579.617 1.543 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 2516 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2787 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2962 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3140 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3558 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1919064 1874.086 1.830 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3859 pick_re_612_> Number of MODEL atoms, selected restraints; 373 4305 pick_re_612_> Number of MODEL atoms, selected restraints; 373 4327 iupac_m_483_> CD1/2 CE1/2 swapped: 90.4340 2 2 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: -90.1560 iupac_m_486_> OE1/2 will be swapped: 164.1423 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 : 4327 4327 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 675 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 : 1488.1776 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 3.7502 1.000 2 Bond angle potential : 520 0 1 2.314 2.314 54.315 1.000 3 Stereochemical cosine torsion poten: 244 0 7 51.701 51.701 96.289 1.000 4 Stereochemical improper torsion pot: 146 0 0 0.996 0.996 3.3521 1.000 5 Soft-sphere overlap restraints : 675 0 0 0.001 0.001 0.10859 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) : 823 0 0 0.235 0.235 229.48 1.000 10 Distance restraints 2 (N-O) : 905 0 1 0.324 0.324 290.54 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 3.817 3.817 9.1076 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 0 60.656 60.656 0.90866 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 0 55.853 55.853 3.9918 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 0 26.657 26.657 3.0889 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 102.778 102.778 1.0040 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) : 852 0 0 0.462 0.462 588.47 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 1 2 22.446 31.200 2.8401 1.000 26 Distance restraints 4 (SDCH-SDCH) : 274 0 1 0.839 0.839 200.93 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_my.V99990001 # Heavy relative violation of each residue is written to: 1fdx_my.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: 4208.7632 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 1309 20V 21N C N 138 140 142.48 -119.90 101.81 3.50 55.90 153.20 16.93 1 21N 21N N CA 140 141 165.88 137.00 39.50 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 0 2 12 13 28 33 42 49 63 51 << end of ENERGY. >> Model assessment by GA341 potential Surface library : /home/tools/modeller-9.16//modlib/surf5.de Pair library : /home/tools/modeller-9.16//modlib/pair9.de Chain identifier : _ % sequence identity : 96.295998 Sequence length : 54 Compactness : 0.649013 Native energy (pair) : -42.801671 Native energy (surface) : -1.334076 Native energy (combined) : -3.402627 Z score (pair) : -3.866796 Z score (surface) : -4.207704 Z score (combined) : -5.639974 GA341 score : 1.000000 openf___224_> Open 1fdx_my.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 openf___224_> Open 1fdx_my.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1919084 1874.105 1.830 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 2516 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2787 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2962 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3140 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3558 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3859 pick_re_612_> Number of MODEL atoms, selected restraints; 373 4305 pick_re_612_> Number of MODEL atoms, selected restraints; 373 4327 iupac_m_486_> OE1/2 will be swapped: 147.0436 17 17 iupac_m_485_> OD1/2 will be swapped: 146.5961 37 37 iupac_m_485_> OD1/2 will be swapped: 128.9440 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 : 4327 4327 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 691 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 : 1521.7859 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 4.1563 1.000 2 Bond angle potential : 520 0 2 2.400 2.400 57.584 1.000 3 Stereochemical cosine torsion poten: 244 0 7 51.669 51.669 96.545 1.000 4 Stereochemical improper torsion pot: 146 0 0 1.027 1.027 3.5586 1.000 5 Soft-sphere overlap restraints : 691 0 0 0.001 0.001 0.15748 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) : 823 0 0 0.241 0.241 232.94 1.000 10 Distance restraints 2 (N-O) : 905 0 1 0.321 0.321 289.60 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 3.861 3.861 9.3185 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 0 74.806 74.806 9.0116 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 0 56.570 56.570 7.5022 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 0 36.261 36.261 3.7708 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 114.799 114.799 0.94107 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) : 852 0 0 0.567 0.567 603.60 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 1 1 22.843 30.582 -0.68597 1.000 26 Distance restraints 4 (SDCH-SDCH) : 274 0 0 0.876 0.876 203.79 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_my.V99990002 # Heavy relative violation of each residue is written to: 1fdx_my.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: 4655.0703 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 1309 20V 21N C N 138 140 135.59 -119.90 107.33 3.84 55.90 145.69 15.94 1 21N 21N N CA 140 141 161.46 137.00 39.50 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 0 3 15 23 21 39 37 64 49 59 << end of ENERGY. >> Model assessment by GA341 potential Surface library : /home/tools/modeller-9.16//modlib/surf5.de Pair library : /home/tools/modeller-9.16//modlib/pair9.de Chain identifier : _ % sequence identity : 96.295998 Sequence length : 54 Compactness : 0.647616 Native energy (pair) : -39.299559 Native energy (surface) : -2.559369 Native energy (combined) : -3.922372 Z score (pair) : -4.153246 Z score (surface) : -4.477515 Z score (combined) : -5.441761 GA341 score : 1.000000 openf___224_> Open 1fdx_my.B99990002.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 >> Summary of successfully produced models: Filename molpdf GA341 score ------------------------------------------------------- 1fdx_my.B99990001.pdb 1488.17761 1.00000 1fdx_my.B99990002.pdb 1521.78589 1.00000 Dynamically allocated memory at finish [B,KiB,MiB]: 1919064 1874.086 1.830 Starting time : 2016/04/05 22:38:15 Closing time : 2016/04/05 22:38:21 Total CPU time [seconds] : 6.39