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 22:38:27 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]: 265619 259.394 0.253 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 267069 260.810 0.255 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269969 263.642 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 330853 323.099 0.316 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 331273 323.509 0.316 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 331485 323.716 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]: 365010 356.455 0.348 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 365010 356.455 0.348 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 365181 356.622 0.348 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 366031 357.452 0.349 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 367289 358.681 0.350 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 369193 360.540 0.352 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 369193 360.540 0.352 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 369283 360.628 0.352 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 372139 363.417 0.355 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 372139 363.417 0.355 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 372274 363.549 0.355 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 376558 367.732 0.359 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 376558 367.732 0.359 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 376756 367.926 0.359 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383182 374.201 0.365 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 383182 374.201 0.365 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383479 374.491 0.366 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 393101 383.888 0.375 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 393101 383.888 0.375 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 393551 384.327 0.375 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 393155 383.940 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]: 532407 519.929 0.508 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 534007 521.491 0.509 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 537987 525.378 0.513 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 539987 527.331 0.515 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 542987 530.261 0.518 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 547487 534.655 0.522 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 553059 540.097 0.527 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 555859 542.831 0.530 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 560059 546.933 0.534 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 566359 553.085 0.540 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 569131 555.792 0.543 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 570531 557.159 0.544 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 578852 565.285 0.552 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 617170 602.705 0.589 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 622594 608.002 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]: 638830 623.857 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]: 656806 641.412 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 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]: 763835 745.933 0.728 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 772027 753.933 0.736 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 788411 769.933 0.752 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 821179 801.933 0.783 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]: 850002 830.080 0.811 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 : 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]: 850018 830.096 0.811 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 58 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 1713 1766 make_re_423_> Number of previous, current selected restraints: 1713 1708 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 850018 830.096 0.811 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 1766 1809 make_re_423_> Number of previous, current selected restraints: 1708 1751 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 850018 830.096 0.811 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 1809 1835 make_re_423_> Number of previous, current selected restraints: 1751 1777 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 850018 830.096 0.811 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]: 882786 862.096 0.842 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]: 882786 862.096 0.842 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 : 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]: 990174 966.967 0.944 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1022942 998.967 0.976 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1088478 1062.967 1.038 make_re_422_> Number of previous, current restraints : 1845 2649 make_re_423_> Number of previous, current selected restraints: 1787 2591 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1121246 1094.967 1.069 make_re_422_> Number of previous, current restraints : 2649 3486 make_re_423_> Number of previous, current selected restraints: 2591 3428 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 3486 4039 make_re_423_> Number of previous, current selected restraints: 3428 3981 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1186782 1158.967 1.132 make_re_422_> Number of previous, current restraints : 4039 4139 make_re_423_> Number of previous, current selected restraints: 3981 4081 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 : 4139 4139 make_re_423_> Number of previous, current selected restraints: 4081 4081 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4139 4139 make_re_423_> Number of previous, current selected restraints: 4081 4081 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4139 4139 make_re_423_> Number of previous, current selected restraints: 4081 4081 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4139 4139 make_re_423_> Number of previous, current selected restraints: 4081 4081 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 : 4139 4139 make_re_423_> Number of previous, current selected restraints: 4081 4081 rmdupl__427_> 314 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 4139 3767 openf___224_> Open 1fdx.rsr openf___224_> Open 1fdx.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1093400 1067.773 1.043 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1191704 1163.773 1.136 rdcsr2__307_> Number of restraints read : 3767 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 3767 3767 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]: 1191724 1163.793 1.137 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 2202 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2459 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2613 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2753 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3106 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1493260 1458.262 1.424 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3367 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3746 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3767 iupac_m_485_> OD1/2 will be swapped: 138.0150 6 6 iupac_m_486_> OE1/2 will be swapped: 135.4959 17 17 iupac_m_485_> OD1/2 will be swapped: -174.3559 31 31 iupac_m_485_> OD1/2 will be swapped: 178.4254 33 33 iupac_m_485_> OD1/2 will be swapped: -138.3375 37 37 >> 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 : 3767 3767 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 694 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 : 427.5174 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 3.6601 1.000 2 Bond angle potential : 520 2 4 2.919 2.919 81.961 1.000 3 Stereochemical cosine torsion poten: 244 0 13 54.840 54.840 102.34 1.000 4 Stereochemical improper torsion pot: 146 0 1 1.924 1.924 10.390 1.000 5 Soft-sphere overlap restraints : 694 0 0 0.005 0.005 1.8255 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 0.371 0.371 42.920 1.000 10 Distance restraints 2 (N-O) : 837 0 3 0.503 0.503 54.673 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 4.928 4.928 15.181 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 1 89.355 89.355 22.076 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 0 75.737 75.737 10.135 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 0 53.660 53.660 4.1515 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 99.960 99.960 1.1142 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 2 0.630 0.630 28.382 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 9 7 30.043 65.649 37.783 1.000 26 Distance restraints 4 (SDCH-SDCH) : 100 0 0 1.032 1.032 10.921 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: 6174.0278 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1296 7S 8C C N 53 55 -51.42 -117.90 67.90 2.09 -63.00 168.78 21.41 1 8C 8C N CA 55 56 127.29 141.10 -41.10 2 1297 8C 9I C N 59 61 -121.50 -120.60 13.10 0.71 -63.40 -177.47 32.05 2 9I 9I N CA 61 62 143.37 130.30 -43.60 3 1298 9I 10A C N 67 69 -71.38 -68.20 29.72 2.51 -62.50 156.90 25.29 3 10A 10A N CA 69 70 115.75 145.30 -40.90 4 1299 10A 11C C N 72 74 -111.38 -63.00 48.44 7.95 -117.90 179.87 6.98 4 11C 11C N CA 74 75 -38.65 -41.10 141.10 5 1302 13A 14C C N 87 89 -114.27 -63.00 94.46 9.92 -63.00 94.46 9.92 5 14C 14C N CA 89 90 38.23 -41.10 -41.10 6 1310 21N 22I C N 146 148 -106.88 -120.60 77.01 3.88 -63.40 107.33 16.43 6 22I 22I N CA 148 149 54.52 130.30 -43.60 7 1313 24Q 25G C N 171 173 106.27 78.70 47.17 0.81 82.20 149.09 8.43 7 25G 25G N CA 173 174 155.63 -166.10 8.50 8 1314 25G 26S C N 175 177 -64.18 -64.10 16.13 1.17 -136.60 173.50 9.79 8 26S 26S N CA 177 178 -51.13 -35.00 151.20 9 1332 43S 44V C N 296 298 -106.02 -62.40 85.95 9.41 -62.40 85.95 9.41 9 44V 44V N CA 298 299 31.66 -42.40 -42.40 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 6 5 29 28 36 38 36 53 56 54 << end of ENERGY. openf___224_> Open 1fdx.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 openf___224_> Open $(LIB)/atmcls-melo.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1493686 1458.678 1.424 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1493750 1458.740 1.425 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1493814 1458.803 1.425 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1493942 1458.928 1.425 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1494134 1459.115 1.425 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1494390 1459.365 1.425 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1494774 1459.740 1.426 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1495350 1460.303 1.426 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1495400 1460.352 1.426 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1495458 1460.408 1.426 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1496354 1461.283 1.427 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1497698 1462.596 1.428 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1497764 1462.660 1.428 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1499748 1464.598 1.430 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1499904 1464.750 1.430 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1502912 1467.688 1.433 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1503206 1467.975 1.434 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1503710 1468.467 1.434 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1504706 1469.439 1.435 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1509186 1473.814 1.439 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1511220 1475.801 1.441 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1515672 1480.148 1.445 openf___224_> Open $(LIB)/melo1-dist.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1516068 1480.535 1.446 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1516864 1481.312 1.447 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1517660 1482.090 1.447 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1518848 1483.250 1.448 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1519248 1483.641 1.449 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1519848 1484.227 1.449 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1520748 1485.105 1.450 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1522096 1486.422 1.452 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1524120 1488.398 1.454 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1524320 1488.594 1.454 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1527356 1491.559 1.457 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1527656 1491.852 1.457 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1532208 1496.297 1.461 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1532656 1496.734 1.462 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1539484 1503.402 1.468 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1540156 1504.059 1.469 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1550400 1514.062 1.479 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1551408 1515.047 1.480 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1552008 1515.633 1.480 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1552408 1516.023 1.480 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1567772 1531.027 1.495 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1569284 1532.504 1.497 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1570184 1533.383 1.497 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1570784 1533.969 1.498 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1593832 1556.477 1.520 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1596100 1558.691 1.522 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1597444 1560.004 1.523 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1598344 1560.883 1.524 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1632916 1594.645 1.557 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1636320 1597.969 1.561 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1638336 1599.938 1.562 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1639684 1601.254 1.564 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1691540 1651.895 1.613 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1696644 1656.879 1.618 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1699668 1659.832 1.621 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1701692 1661.809 1.623 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1779476 1737.770 1.697 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1787132 1745.246 1.704 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1791668 1749.676 1.709 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1794704 1752.641 1.712 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1911380 1866.582 1.823 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 0 0 0 0 820 openf___224_> Open 1fdx.B99990001.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1911380 1866.582 1.823 read_mo_297_> Segments, residues, atoms: 1 54 373 read_mo_298_> Segment: 1 1 54 373 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1913478 1868.631 1.825 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1943074 1897.533 1.853 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1943724 1898.168 1.854 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1973320 1927.070 1.882 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 54 372 378 0 0 150 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 54 372 378 518 628 150 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 openf___224_> Open 1fdx.B99990001.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1984273 1937.767 1.892 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1984349 1937.841 1.892 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1984520 1938.008 1.893 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1985370 1938.838 1.893 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1986628 1940.066 1.895 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1988532 1941.926 1.896 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1988572 1941.965 1.896 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1988662 1942.053 1.897 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1991518 1944.842 1.899 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1991578 1944.900 1.899 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1991713 1945.032 1.899 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1995997 1949.216 1.904 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1996085 1949.302 1.904 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1996283 1949.495 1.904 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2029915 1982.339 1.936 read_mo_297_> Segments, residues, atoms: 1 54 373 read_mo_298_> Segment: 1 1 54 373 # ALGNMT CODE 1 1fdx 2 1fdx 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: 373 0 openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1975302 1929.006 1.884 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1976752 1930.422 1.885 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1979652 1933.254 1.888 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 2040536 1992.711 1.946 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2040956 1993.121 1.946 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2041168 1993.328 1.947 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 28 atoms selected for loop refinement make_re_417_> Restraint type to be calculated: bond r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 30 0 0 0 Total number of restraints before, now : 0 30 make_re_422_> Number of previous, current restraints : 0 30 make_re_423_> Number of previous, current selected restraints: 0 30 make_re_417_> Restraint type to be calculated: angle r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 44 0 0 Total number of restraints before, now : 30 74 make_re_422_> Number of previous, current restraints : 30 74 make_re_423_> Number of previous, current selected restraints: 30 74 make_re_417_> Restraint type to be calculated: improper r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 0 0 12 Total number of restraints before, now : 74 86 make_re_422_> Number of previous, current restraints : 74 86 make_re_423_> Number of previous, current selected restraints: 74 86 make_re_417_> Restraint type to be calculated: dihedral r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 0 56 0 Total number of restraints before, now : 86 142 make_re_422_> Number of previous, current restraints : 86 142 make_re_423_> Number of previous, current selected restraints: 86 142 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1973320 1927.070 1.882 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 142 150 make_re_423_> Number of previous, current selected restraints: 142 150 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1973336 1927.086 1.882 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 6 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 150 156 make_re_423_> Number of previous, current selected restraints: 150 150 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1973336 1927.086 1.882 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 156 160 make_re_423_> Number of previous, current selected restraints: 150 154 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1973336 1927.086 1.882 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 160 162 make_re_423_> Number of previous, current selected restraints: 154 156 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1973336 1927.086 1.882 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 162 162 make_re_423_> Number of previous, current selected restraints: 156 156 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1973336 1927.086 1.882 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: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 162 162 make_re_423_> Number of previous, current selected restraints: 156 156 pick_re_612_> Number of MODEL atoms, selected restraints; 28 162 rmdupl__427_> 30 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 162 132 openf___224_> Open 1fdx.lrsr preppdf_457W> Both soft sphere and statistical potential terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 28 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 132 132 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 784 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 : 7.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 57.6728 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 : 30 0 0 0.005 0.005 0.22778 1.000 2 Bond angle potential : 44 0 1 2.838 2.838 7.1696 1.000 3 Stereochemical cosine torsion poten: 26 0 0 40.076 40.076 7.7435 1.000 4 Stereochemical improper torsion pot: 12 0 0 1.086 1.086 0.35752 1.000 5 Soft-sphere overlap restraints : 784 0 0 0.001 0.001 0.36325E-01 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 6 0 0 6.868 6.868 3.3402 1.000 14 Sidechain Chi_1 dihedral restraints: 4 0 0 97.984 97.984 2.2381 1.000 15 Sidechain Chi_2 dihedral restraints: 2 0 0 92.171 92.171 0.43751 1.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 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) : 0 0 0 0.000 0.000 0.0000 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: 8 3 1 26.284 103.213 7.4684 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 : 784 0 8 1.754 1.754 28.654 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 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 1 116 9I 10A C N 67 69 -71.40 -68.20 29.68 2.51 -62.50 156.94 25.31 1 10A 10A N CA 69 70 115.79 145.30 -40.90 2 117 24Q 25G C N 171 173 106.29 78.70 47.18 0.81 82.20 149.09 8.43 2 25G 25G N CA 173 174 155.63 -166.10 8.50 3 120 27I 28Y C N 189 191 -67.21 -98.40 32.19 1.39 -63.50 179.78 28.35 3 28Y 28Y N CA 191 192 136.34 128.40 -43.40 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 6 5 29 28 36 38 36 53 57 53 << end of ENERGY. openf___224_> Open 1fdx.IL00000001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 openf___224_> Open 1fdx.IL00000001.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2265968 2212.859 2.161 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 28 1 5.0000 randomi_496_> Amplitude is > 0; randomization is done. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 28 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 132 132 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 748 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 : 7.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 35.5266 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 : 30 0 0 0.007 0.007 0.36023 1.000 2 Bond angle potential : 44 0 0 3.199 3.199 9.4725 1.000 3 Stereochemical cosine torsion poten: 26 0 0 39.806 39.806 7.7545 1.000 4 Stereochemical improper torsion pot: 12 0 0 1.271 1.271 0.49867 1.000 5 Soft-sphere overlap restraints : 748 0 0 0.000 0.000 0.0000 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 6 0 0 8.297 8.297 4.8742 1.000 14 Sidechain Chi_1 dihedral restraints: 4 0 0 97.583 97.583 1.1831 1.000 15 Sidechain Chi_2 dihedral restraints: 2 0 0 4.515 4.515 -0.46639 1.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 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) : 0 0 0 0.000 0.000 0.0000 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: 8 3 1 25.640 102.190 6.8100 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 : 748 0 3 1.741 1.741 5.0399 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 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 1 116 9I 10A C N 67 69 -68.74 -68.20 29.52 2.40 -62.50 156.81 25.41 1 10A 10A N CA 69 70 115.79 145.30 -40.90 2 117 24Q 25G C N 171 173 106.29 78.70 47.53 0.81 82.20 148.66 8.41 2 25G 25G N CA 173 174 155.20 -166.10 8.50 3 120 27I 28Y C N 189 191 -72.57 -98.40 27.02 1.23 -63.50 179.97 28.11 3 28Y 28Y N CA 191 192 136.34 128.40 -43.40 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 6 4 26 27 34 42 32 50 57 53 << end of ENERGY. openf___224_> Open 1fdx.BL00010001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 openf___224_> Open 1fdx.IL00000001.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2265968 2212.859 2.161 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 28 1 5.0000 randomi_496_> Amplitude is > 0; randomization is done. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 28 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 132 132 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 731 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 : 7.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 36.1138 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 : 30 0 0 0.007 0.007 0.35110 1.000 2 Bond angle potential : 44 0 1 3.167 3.167 9.4453 1.000 3 Stereochemical cosine torsion poten: 26 0 0 40.433 40.433 7.9393 1.000 4 Stereochemical improper torsion pot: 12 0 0 1.317 1.317 0.50901 1.000 5 Soft-sphere overlap restraints : 731 0 0 0.000 0.000 0.0000 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 6 0 0 8.263 8.263 4.8351 1.000 14 Sidechain Chi_1 dihedral restraints: 4 0 0 77.347 77.347 1.0521 1.000 15 Sidechain Chi_2 dihedral restraints: 2 0 0 1.895 1.895 -0.53582 1.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 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) : 0 0 0 0.000 0.000 0.0000 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: 8 3 1 25.394 102.114 6.5778 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 : 731 0 3 1.749 1.749 5.9400 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 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 1 116 9I 10A C N 67 69 -67.25 -68.20 29.53 2.35 -62.50 156.76 25.47 1 10A 10A N CA 69 70 115.79 145.30 -40.90 2 117 24Q 25G C N 171 173 106.29 78.70 47.63 0.81 82.20 148.55 8.40 2 25G 25G N CA 173 174 155.08 -166.10 8.50 3 120 27I 28Y C N 189 191 -73.40 -98.40 26.23 1.20 -63.50 -179.98 28.07 3 28Y 28Y N CA 191 192 136.34 128.40 -43.40 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 6 4 28 27 34 40 33 48 56 54 << end of ENERGY. openf___224_> Open 1fdx.BL00020001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 openf___224_> Open 1fdx.IL00000001.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2265968 2212.859 2.161 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 28 1 5.0000 randomi_496_> Amplitude is > 0; randomization is done. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 28 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 132 132 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 721 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 : 7.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 36.1129 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 : 30 0 0 0.009 0.009 0.68894 1.000 2 Bond angle potential : 44 0 1 3.543 3.543 11.609 1.000 3 Stereochemical cosine torsion poten: 26 0 0 41.825 41.825 7.9908 1.000 4 Stereochemical improper torsion pot: 12 0 0 1.341 1.341 0.56267 1.000 5 Soft-sphere overlap restraints : 721 0 0 0.000 0.000 0.0000 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 6 0 0 6.581 6.581 3.0667 1.000 14 Sidechain Chi_1 dihedral restraints: 4 0 0 88.156 88.156 -0.58653E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 2 0 0 4.264 4.264 -0.43251 1.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 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) : 0 0 0 0.000 0.000 0.0000 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: 8 3 0 26.167 103.203 7.1563 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 : 721 0 2 1.775 1.775 5.5296 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 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 1 116 9I 10A C N 67 69 -66.53 -68.20 29.56 2.32 -62.50 156.74 25.50 1 10A 10A N CA 69 70 115.79 145.30 -40.90 2 117 24Q 25G C N 171 173 106.29 78.70 45.90 0.81 82.20 150.66 8.50 2 25G 25G N CA 173 174 157.22 -166.10 8.50 3 120 27I 28Y C N 189 191 -65.51 -98.40 33.84 1.44 -63.50 179.76 28.43 3 28Y 28Y N CA 191 192 136.34 128.40 -43.40 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 6 4 26 28 32 38 34 50 59 53 << end of ENERGY. openf___224_> Open 1fdx.BL00030001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 openf___224_> Open 1fdx.IL00000001.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2265968 2212.859 2.161 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 28 1 5.0000 randomi_496_> Amplitude is > 0; randomization is done. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 28 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 132 132 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 797 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 : 7.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 71.1613 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 : 30 0 0 0.017 0.017 2.6471 1.000 2 Bond angle potential : 44 1 2 5.922 5.922 27.088 1.000 3 Stereochemical cosine torsion poten: 26 0 1 51.044 51.044 10.740 1.000 4 Stereochemical improper torsion pot: 12 0 1 2.560 2.560 2.4722 1.000 5 Soft-sphere overlap restraints : 797 0 0 0.000 0.000 0.0000 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 6 0 0 6.928 6.928 3.3990 1.000 14 Sidechain Chi_1 dihedral restraints: 4 0 0 72.117 72.117 1.3297 1.000 15 Sidechain Chi_2 dihedral restraints: 2 0 0 91.209 91.209 0.50382 1.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 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) : 0 0 0 0.000 0.000 0.0000 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: 8 4 1 48.658 137.672 11.952 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 : 797 0 4 1.761 1.761 11.030 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 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 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 73 27I 28Y C N 189 191 150.59 120.00 30.59 6.95 120.00 30.59 6.95 ------------------------------------------------------------------------------------------------- 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 1 116 9I 10A C N 67 69 -65.31 -68.20 29.65 2.29 -62.50 156.71 25.55 1 10A 10A N CA 69 70 115.79 145.30 -40.90 2 117 24Q 25G C N 171 173 106.29 78.70 35.80 0.94 82.20 164.36 9.17 2 25G 25G N CA 173 174 171.09 -166.10 8.50 3 119 26S 27I C N 181 183 -66.41 -63.40 5.96 0.91 -120.60 177.24 8.16 3 27I 27I N CA 183 184 -38.46 -43.60 130.30 4 120 27I 28Y C N 189 191 113.96 -124.30 121.74 9.12 -63.50 -107.41 47.63 4 28Y 28Y N CA 191 192 136.34 135.40 -43.40 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 6 4 28 27 32 39 36 49 57 54 << end of ENERGY. openf___224_> Open 1fdx.BL00040001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 >> Summary of successfully produced models: Filename molpdf ---------------------------------------- 1fdx.B99990001.pdb 427.51736 >> Summary of successfully produced loop models: Filename molpdf ---------------------------------------- 1fdx.BL00010001.pdb 35.52662 1fdx.BL00020001.pdb 36.11380 1fdx.BL00030001.pdb 36.11290 1fdx.BL00040001.pdb 71.16129 Dynamically allocated memory at finish [B,KiB,MiB]: 2203992 2152.336 2.102 Starting time : 2016/04/05 22:38:27 Closing time : 2016/04/05 22:38:35 Total CPU time [seconds] : 7.24