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 22:38:42 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_allh.lib read_to_681_> topology.submodel read from topology file: 1 openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 604455 590.288 0.576 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 606055 591.851 0.578 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 610035 595.737 0.582 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 612035 597.690 0.584 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 615035 600.620 0.587 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 619535 605.015 0.591 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 625107 610.456 0.596 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 627907 613.190 0.599 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 632107 617.292 0.603 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 638407 623.444 0.609 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 641179 626.151 0.611 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 642579 627.519 0.613 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 650900 635.645 0.621 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 723420 706.465 0.690 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 732548 715.379 0.699 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 1 1 atom names : N -C CA H atom indices : 1 0 3 2 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 54 721 727 0 0 206 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 779240 760.977 0.743 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 811280 792.266 0.774 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 811436 792.418 0.774 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 54 723 729 1321 1939 206 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 811508 792.488 0.774 patch_______> segment topology patched using RTF: 54 ; ASP ; CTER segments residues atoms bonds angles dihedrals impropers: 1 54 724 730 1323 1942 207 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 54 724 730 1323 1942 207 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: 322 402 openf___224_> Open 1fdx.ini wrpdb___568_> Residues, atoms, selected atoms: 54 724 724 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 918537 897.009 0.876 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 926729 905.009 0.884 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 943113 921.009 0.899 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 975881 953.009 0.931 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1008649 985.009 0.962 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1074185 1049.009 1.024 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1106953 1081.009 1.056 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 730 1323 1630 202 Total number of restraints before, now : 0 3885 make_re_422_> Number of previous, current restraints : 0 3885 make_re_423_> Number of previous, current selected restraints: 0 3885 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1147710 1120.811 1.095 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 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1180494 1152.826 1.126 make_re_422_> Number of previous, current restraints : 3885 3937 make_re_423_> Number of previous, current selected restraints: 3885 3937 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1180494 1152.826 1.126 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 : 3937 3990 make_re_423_> Number of previous, current selected restraints: 3937 3932 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1180494 1152.826 1.126 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 : 3990 4033 make_re_423_> Number of previous, current selected restraints: 3932 3975 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1180494 1152.826 1.126 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 : 4033 4059 make_re_423_> Number of previous, current selected restraints: 3975 4001 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1180494 1152.826 1.126 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 : 4059 4068 make_re_423_> Number of previous, current selected restraints: 4001 4010 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1180494 1152.826 1.126 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 : 4068 4069 make_re_423_> Number of previous, current selected restraints: 4010 4011 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1388970 1356.416 1.325 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1454506 1420.416 1.387 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1585578 1548.416 1.512 make_re_422_> Number of previous, current restraints : 4069 4873 make_re_423_> Number of previous, current selected restraints: 4011 4815 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1651114 1612.416 1.575 make_re_422_> Number of previous, current restraints : 4873 5710 make_re_423_> Number of previous, current selected restraints: 4815 5652 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1716650 1676.416 1.637 make_re_422_> Number of previous, current restraints : 5710 6263 make_re_423_> Number of previous, current selected restraints: 5652 6205 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 6263 6363 make_re_423_> Number of previous, current selected restraints: 6205 6305 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 : 6363 6363 make_re_423_> Number of previous, current selected restraints: 6305 6305 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 6363 6363 make_re_423_> Number of previous, current selected restraints: 6305 6305 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 6363 6363 make_re_423_> Number of previous, current selected restraints: 6305 6305 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 6363 6363 make_re_423_> Number of previous, current selected restraints: 6305 6305 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 : 6363 6363 make_re_423_> Number of previous, current selected restraints: 6305 6305 rmdupl__427_> 350 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 6363 5955 openf___224_> Open 1fdx.rsr openf___224_> Open 1fdx.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1676870 1637.568 1.599 rdcsr2__307_> Number of restraints read : 5955 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 5955 5955 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]: 1676890 1637.588 1.599 read_mo_297_> Segments, residues, atoms: 1 54 724 read_mo_298_> Segment: 1 1 54 724 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 724 724 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 724 4390 pick_re_612_> Number of MODEL atoms, selected restraints; 724 4647 pick_re_612_> Number of MODEL atoms, selected restraints; 724 4801 pick_re_612_> Number of MODEL atoms, selected restraints; 724 4941 pick_re_612_> Number of MODEL atoms, selected restraints; 724 5294 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1986850 1940.283 1.895 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2004226 1957.252 1.911 pick_re_612_> Number of MODEL atoms, selected restraints; 724 5555 pick_re_612_> Number of MODEL atoms, selected restraints; 724 5934 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2038978 1991.189 1.945 pick_re_612_> Number of MODEL atoms, selected restraints; 724 5955 iupac_m_486_> OE1/2 will be swapped: -109.9459 17 17 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: -109.9459 iupac_m_483_> CD1/2 CE1/2 swapped: 105.7504 28 28 iupac_m_485_> OD1/2 will be swapped: 123.7144 54 54 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: 123.7144 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 724 724 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 5955 5955 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3881 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 : 831.6525 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 : 730 0 0 0.004 0.004 3.4500 1.000 2 Bond angle potential : 1323 31 42 4.819 4.819 415.61 1.000 3 Stereochemical cosine torsion poten: 1222 0 12 28.591 28.591 159.37 1.000 4 Stereochemical improper torsion pot: 202 10 11 5.287 5.287 94.643 1.000 5 Soft-sphere overlap restraints : 3881 0 0 0.001 0.001 0.39723 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 0.305 0.305 22.684 1.000 10 Distance restraints 2 (N-O) : 837 0 3 0.497 0.497 54.938 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 4.620 4.620 13.340 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 0 60.646 60.646 4.8792 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 0 69.462 69.462 9.7658 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 0 42.195 42.195 2.7258 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 4.104 4.104 0.24220 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 0.482 0.482 11.146 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 7 32.336 64.237 31.561 1.000 26 Distance restraints 4 (SDCH-SDCH) : 100 0 0 0.992 0.992 6.8938 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.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: 6579.8120 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 3482 5N 6D C N 81 83 -74.20 -70.90 24.19 1.03 -63.30 146.15 18.72 1 6D 6D N CA 83 85 174.26 150.30 -40.00 2 3483 6D 7S C N 93 95 84.92 56.90 52.26 2.33 -64.10 151.50 20.10 2 7S 7S N CA 95 97 -7.72 36.40 -35.00 3 3484 7S 8C C N 104 106 -71.84 -117.90 58.99 1.60 -63.00 145.61 17.17 3 8C 8C N CA 106 108 104.24 141.10 -41.10 4 3485 8C 9I C N 115 117 -95.31 -97.30 78.27 8.16 -63.40 97.91 15.12 4 9I 9I N CA 117 119 48.96 127.20 -43.60 5 3486 9I 10A C N 134 136 49.83 55.40 6.48 0.47 -62.50 139.33 28.23 5 10A 10A N CA 136 138 41.53 38.20 -40.90 6 3488 11C 12G C N 155 157 -133.13 -62.40 101.82 14.30 82.20 146.58 10.59 6 12G 12G N CA 157 159 32.05 -41.20 8.50 7 3501 24Q 25G C N 344 346 -76.65 -80.20 12.94 0.35 82.20 -139.34 7.04 7 25G 25G N CA 346 348 161.66 174.10 8.50 report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 14 486 1.458 serious non-bonded atom clash: 26 511 1.326 serious non-bonded atom clash: 191 211 1.499 serious non-bonded atom clash: 299 434 1.402 serious non-bonded atom clash: 324 389 1.466 serious non-bonded atom clash: 496 521 1.436 serious non-bonded atom clash: 650 659 1.489 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: 68 43 58 76 98 120 138 150 132 166 188 218 203 232 252 << end of ENERGY. openf___224_> Open 1fdx.B99990004.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 724 724 >> Summary of successfully produced models: Filename molpdf ---------------------------------------- 1fdx.B99990004.pdb 831.65247 Dynamically allocated memory at finish [B,KiB,MiB]: 2038978 1991.189 1.945 Starting time : 2016/04/05 22:38:42 Closing time : 2016/04/05 22:38:48 Total CPU time [seconds] : 4.49