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 22:39:35 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 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 763274 745.385 0.728 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 771466 753.385 0.736 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 787850 769.385 0.751 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 826978 807.596 0.789 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 961130 938.604 0.917 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 961166 938.639 0.917 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1521510 1485.850 1.451 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1678790 1639.443 1.601 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1749358 1708.357 1.668 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1863802 1820.119 1.777 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1893186 1848.814 1.805 make_re_422_> Number of previous, current restraints : 1230 2034 make_re_423_> Number of previous, current selected restraints: 1230 2034 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1925970 1880.830 1.837 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1991506 1944.830 1.899 make_re_422_> Number of previous, current restraints : 2034 2871 make_re_423_> Number of previous, current selected restraints: 2034 2871 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2024274 1976.830 1.930 make_re_422_> Number of previous, current restraints : 2871 3424 make_re_423_> Number of previous, current selected restraints: 2871 3424 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 3424 3524 make_re_423_> Number of previous, current selected restraints: 3424 3524 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 : 3524 3524 make_re_423_> Number of previous, current selected restraints: 3524 3524 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 3524 3524 make_re_423_> Number of previous, current selected restraints: 3524 3524 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 3524 3524 make_re_423_> Number of previous, current selected restraints: 3524 3524 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 3524 3524 make_re_423_> Number of previous, current selected restraints: 3524 3524 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 : 3524 3524 make_re_423_> Number of previous, current selected restraints: 3524 3524 condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 3524 3524 openf___224_> Open 1fdx.rsr openf___224_> Open 1fdx.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1930892 1885.637 1.841 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2029196 1981.637 1.935 rdcsr2__307_> Number of restraints read : 3524 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 3524 3524 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]: 2029216 1981.656 1.935 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 1959 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2216 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2370 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2510 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2863 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2330752 2276.125 2.223 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3124 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3503 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3524 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2339704 2284.867 2.231 iupac_m_485_> OD1/2 will be swapped: -105.0219 31 31 iupac_m_485_> OD1/2 will be swapped: 110.8994 33 33 iupac_m_485_> OD1/2 will be swapped: 104.1889 37 37 iupac_m_485_> OD1/2 will be swapped: 163.2374 54 54 iupac_m_484W> Dihedral still outside +-90: 157.3281 >> 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 : 3524 3524 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 585 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 : 8490.7236 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 : 378 0 0 0.005 0.005 14.529 1.000 2 Bond angle potential : 518 5 30 4.257 4.257 583.33 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 150 1 3 14.200 14.200 6179.8 1.000 5 Soft-sphere overlap restraints : 585 0 3 0.021 0.021 29.115 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 4 39 1.042 1.042 415.25 1.000 10 Distance restraints 2 (N-O) : 837 8 72 1.221 1.221 548.56 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 16 16 28.052 53.957 277.16 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 10 20.318 80.648 68.898 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 7 77.759 77.759 36.790 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 0 70.920 70.920 5.3413 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 1.092 1.092 0.81161E-02 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 10 1.100 1.100 104.14 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 0 37 0.000 0.000 154.18 1.000 26 Distance restraints 4 (SDCH-SDCH) : 100 2 13 2.528 2.528 73.652 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: 11368.3125 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 1 528 54D 54D CB CG 367 368 147.98 118.77 29.21 12.90 118.77 29.21 12.90 ------------------------------------------------------------------------------------------------- Feature 9 : Distance restraints 1 (CA-CA) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1504 10A 47V CA CA 70 319 10.97 8.45 2.51 4.71 8.45 2.51 4.71 2 1526 11C 47V CA CA 75 319 11.40 7.93 3.47 6.80 7.93 3.47 6.80 3 1680 17E 44V CA CA 112 299 10.43 7.84 2.59 4.92 7.84 2.59 4.92 4 1826 27I 47V CA CA 184 319 14.60 11.64 2.96 4.56 11.64 2.96 4.56 ------------------------------------------------------------------------------------------------- Feature 10 : Distance restraints 2 (N-O) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 2204 11C 47V N O 74 324 12.65 9.53 3.13 4.86 9.53 3.13 4.86 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1048 10A 10A CA C 70 72 -1.05 0.00 -1.05 -0.46 179.80 179.15 77.97 2 1054 8C 8C CA C 56 59 -112.10 179.80 68.10 29.64 179.80 68.10 29.64 3 1057 18C 18C CA C 121 124 -110.29 179.80 69.91 30.43 179.80 69.91 30.43 4 1059 38C 38C CA C 266 269 -3.49 0.00 -3.49 -1.52 179.80 176.71 76.91 5 1061 45C 45C CA C 306 309 -151.56 179.80 28.64 12.47 179.80 28.64 12.47 6 1062 6D 6D CA C 42 47 -43.46 0.00 -43.46 -18.92 179.80 136.74 59.52 7 1066 17E 17E CA C 112 118 -115.21 179.80 64.99 28.29 179.80 64.99 28.29 8 1076 27I 27I CA C 184 189 -117.09 179.80 63.11 27.47 179.80 63.11 27.47 9 1094 3V 3V CA C 19 23 -143.49 179.80 36.71 15.98 179.80 36.71 15.98 10 1095 20V 20V CA C 134 138 -111.64 179.80 68.56 29.84 179.80 68.56 29.84 ------------------------------------------------------------------------------------------------- Feature 26 : Distance restraints 4 (SDCH-SDCH) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 3471 11C 46P SG CB 77 314 10.76 4.04 6.72 4.54 4.04 6.72 4.54 2 3519 45C 47V SG CB 308 320 8.64 3.66 4.98 4.51 3.66 4.98 4.51 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 4 22 20 19 18 36 29 32 37 44 << end of ENERGY. >> Model assessment by GA341 potential Surface library : /home/tools/modeller-9.16//modlib/surf5.de Pair library : /home/tools/modeller-9.16//modlib/pair9.de Chain identifier : _ % sequence identity : 37.036999 Sequence length : 54 Compactness : 0.643464 Native energy (pair) : -14.245276 Native energy (surface) : 0.559455 Native energy (combined) : -0.820984 Z score (pair) : -3.914810 Z score (surface) : -3.097647 Z score (combined) : -4.731410 GA341 score : 0.999689 openf___224_> Open 1fdx.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 openf___224_> Open 1fdx.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2339724 2284.887 2.231 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 1959 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2216 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2370 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2510 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2863 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3124 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3503 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3524 iupac_m_485_> OD1/2 will be swapped: -98.2823 33 33 iupac_m_485_> OD1/2 will be swapped: -128.7079 37 37 iupac_m_485_> OD1/2 will be swapped: 149.9863 54 54 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 373 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 3524 3524 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 760 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 : 2678.7300 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 : 378 0 0 0.006 0.006 23.502 1.000 2 Bond angle potential : 518 4 29 3.077 3.077 245.63 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 150 0 3 1.999 1.999 32.761 1.000 5 Soft-sphere overlap restraints : 760 2 9 0.024 0.024 50.950 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 13 105 1.259 1.259 682.65 1.000 10 Distance restraints 2 (N-O) : 837 12 94 1.355 1.355 726.70 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 20 21 31.312 53.242 415.29 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 13 21.961 89.413 80.321 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 11 79.575 79.575 41.626 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 1 59.831 59.831 7.4368 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 125.757 125.757 1.9697 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 6 1.025 1.025 89.842 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 0 40 0.000 0.000 174.44 1.000 26 Distance restraints 4 (SDCH-SDCH) : 100 4 12 2.825 2.825 105.62 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.V99990002 # Heavy relative violation of each residue is written to: 1fdx.V99990002 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 12331.3594 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 1 546 17E 17E CA N 112 111 132.53 121.32 11.21 4.65 121.32 11.21 4.65 ------------------------------------------------------------------------------------------------- Feature 9 : Distance restraints 1 (CA-CA) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1557 13A 16P CA CA 85 105 8.54 5.95 2.59 4.60 5.95 2.59 4.60 2 1615 15K 18C CA CA 96 121 6.80 5.41 1.38 4.57 5.41 1.38 4.57 3 1686 18C 22I CA CA 121 149 9.09 7.19 1.90 4.79 7.19 1.90 4.79 4 1718 19P 38C CA CA 127 266 11.72 8.42 3.30 6.25 8.42 3.30 6.25 5 1764 22I 31D CA CA 149 217 7.32 5.39 1.93 4.51 5.39 1.93 4.51 6 1783 23I 31D CA CA 157 217 8.63 6.26 2.36 4.80 6.26 2.36 4.80 7 1826 27I 47V CA CA 184 319 15.16 11.64 3.52 5.43 11.64 3.52 5.43 8 1877 31D 34S CA CA 217 238 7.99 5.56 2.43 5.41 5.56 2.43 5.41 9 1939 37D 52P CA CA 258 350 10.57 7.70 2.87 5.13 7.70 2.87 5.13 ------------------------------------------------------------------------------------------------- Feature 10 : Distance restraints 2 (N-O) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 2280 16P 13A N O 104 88 5.78 3.16 2.63 5.11 3.16 2.63 5.11 2 2293 17E 13A N O 111 88 7.09 4.27 2.82 5.94 4.27 2.82 5.94 3 2502 31D 22I N O 216 155 5.27 2.82 2.45 6.38 2.82 2.45 6.38 4 2547 34S 31D N O 237 223 6.21 3.09 3.12 7.43 3.09 3.12 7.43 5 2560 35C 31D N O 243 223 5.30 3.11 2.19 6.76 3.11 2.19 6.76 6 2589 37D 32A N O 257 228 10.41 7.05 3.35 5.63 7.05 3.35 5.63 7 2604 38C 32A N O 265 228 13.28 9.83 3.45 5.44 9.83 3.45 5.44 8 2752 47V 5N N O 318 40 13.15 9.10 4.05 7.54 9.10 4.05 7.54 9 2800 50P 3V N O 334 24 7.31 4.44 2.87 5.74 4.44 2.87 5.74 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1049 13A 13A CA C 85 87 -130.04 179.80 50.16 21.83 179.80 50.16 21.83 2 1056 14C 14C CA C 90 93 -152.80 179.80 27.40 11.93 179.80 27.40 11.93 3 1062 6D 6D CA C 42 47 -154.39 179.80 25.81 11.23 179.80 25.81 11.23 4 1067 53E 53E CA C 357 363 -164.58 179.80 15.62 6.80 179.80 15.62 6.80 5 1071 48G 48G CA C 326 327 -89.51 0.00 -89.51 -38.96 179.80 90.69 39.47 6 1076 27I 27I CA C 184 189 -107.15 179.80 73.05 31.80 179.80 73.05 31.80 7 1080 5N 5N CA C 34 39 -48.58 0.00 -48.58 -21.14 179.80 131.62 57.29 8 1083 16P 16P CA C 105 109 -160.94 179.80 19.26 8.38 179.80 19.26 8.38 9 1086 50P 50P CA C 335 339 -48.48 0.00 -48.48 -21.10 179.80 131.72 57.33 10 1088 24Q 24Q CA C 165 171 -59.56 0.00 -59.56 -25.92 179.80 120.64 52.51 11 1095 20V 20V CA C 134 138 -103.80 179.80 76.40 33.25 179.80 76.40 33.25 12 1098 2Y 2Y CA C 7 16 -143.76 179.80 36.44 15.86 179.80 36.44 15.86 ------------------------------------------------------------------------------------------------- Feature 26 : Distance restraints 4 (SDCH-SDCH) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 3483 19P 38C CD CB 128 267 11.78 4.99 6.78 4.69 4.99 6.78 4.69 2 3484 19P 38C CD SG 128 268 10.97 3.83 7.13 5.26 3.83 7.13 5.26 3 3488 19P 38C CG CB 130 267 13.16 4.74 8.41 5.89 4.74 8.41 5.89 4 3489 19P 38C CG SG 130 268 12.28 4.12 8.16 5.92 4.12 8.16 5.92 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 1 2 6 19 26 28 40 40 53 37 41 44 << end of ENERGY. >> Model assessment by GA341 potential Surface library : /home/tools/modeller-9.16//modlib/surf5.de Pair library : /home/tools/modeller-9.16//modlib/pair9.de Chain identifier : _ % sequence identity : 37.036999 Sequence length : 54 Compactness : 0.678066 Native energy (pair) : -8.946956 Native energy (surface) : -2.313385 Native energy (combined) : -1.743465 Z score (pair) : -4.262415 Z score (surface) : -3.704634 Z score (combined) : -5.104085 GA341 score : 0.999995 openf___224_> Open 1fdx.B99990002.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]: 2340130 2285.283 2.232 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2340194 2285.346 2.232 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2340258 2285.408 2.232 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2340386 2285.533 2.232 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2340578 2285.721 2.232 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2340834 2285.971 2.232 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2341218 2286.346 2.233 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2341794 2286.908 2.233 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2341844 2286.957 2.233 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2341902 2287.014 2.233 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2342798 2287.889 2.234 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2344142 2289.201 2.236 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2344208 2289.266 2.236 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2346192 2291.203 2.238 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2346348 2291.355 2.238 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2349356 2294.293 2.241 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2349650 2294.580 2.241 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2350154 2295.072 2.241 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2351150 2296.045 2.242 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2355630 2300.420 2.247 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2357664 2302.406 2.248 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2362116 2306.754 2.253 openf___224_> Open $(LIB)/melo1-dist.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2362512 2307.141 2.253 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2363308 2307.918 2.254 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2364104 2308.695 2.255 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2365292 2309.855 2.256 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2365692 2310.246 2.256 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2366292 2310.832 2.257 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2367192 2311.711 2.258 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2368540 2313.027 2.259 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2370564 2315.004 2.261 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2370764 2315.199 2.261 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2373800 2318.164 2.264 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2374100 2318.457 2.264 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2378652 2322.902 2.268 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2379100 2323.340 2.269 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2385928 2330.008 2.275 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2386600 2330.664 2.276 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2396844 2340.668 2.286 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2397852 2341.652 2.287 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2398452 2342.238 2.287 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2398852 2342.629 2.288 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2414216 2357.633 2.302 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2415728 2359.109 2.304 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2416628 2359.988 2.305 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2417228 2360.574 2.305 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2440276 2383.082 2.327 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2442544 2385.297 2.329 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2443888 2386.609 2.331 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2444788 2387.488 2.332 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2479360 2421.250 2.365 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2482764 2424.574 2.368 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2484780 2426.543 2.370 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2486128 2427.859 2.371 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2537984 2478.500 2.420 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2543088 2483.484 2.425 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2546112 2486.438 2.428 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2548136 2488.414 2.430 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2625920 2564.375 2.504 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2633576 2571.852 2.512 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2638112 2576.281 2.516 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2641148 2579.246 2.519 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2757824 2693.188 2.630 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]: 2757824 2693.188 2.630 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]: 2759922 2695.236 2.632 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2789518 2724.139 2.660 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 2790168 2724.773 2.661 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2819764 2753.676 2.689 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]: 2830717 2764.372 2.700 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2830793 2764.446 2.700 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2830964 2764.613 2.700 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2831814 2765.443 2.701 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2833072 2766.672 2.702 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2834976 2768.531 2.704 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2835016 2768.570 2.704 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2835106 2768.658 2.704 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2837962 2771.447 2.706 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2838022 2771.506 2.707 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2838157 2771.638 2.707 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2842441 2775.821 2.711 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2842529 2775.907 2.711 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2842727 2776.101 2.711 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2876359 2808.944 2.743 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]: 2821746 2755.611 2.691 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 2823196 2757.027 2.692 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 2826096 2759.859 2.695 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 2886980 2819.316 2.753 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2887400 2819.727 2.754 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2887612 2819.934 2.754 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 pick_re_612_> Number of MODEL atoms, selected restraints; 28 106 condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 106 106 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 : 106 106 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 752 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 : 119.2581 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 0.004 0.004 0.89472 1.000 2 Bond angle potential : 44 0 0 1.404 1.404 4.5664 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 12 0 0 0.711 0.711 0.52941 1.000 5 Soft-sphere overlap restraints : 752 0 0 0.002 0.002 0.35674 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 3 3 40.007 40.007 68.279 1.000 14 Sidechain Chi_1 dihedral restraints: 4 0 0 11.413 102.609 4.2652 1.000 15 Sidechain Chi_2 dihedral restraints: 2 0 1 65.801 65.801 3.7206 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 0 7 0.000 0.000 26.130 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 : 752 0 4 1.769 1.769 10.516 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 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 87 8C 8C CA C 56 59 -112.14 179.80 68.06 29.59 179.80 68.06 29.59 2 90 27I 27I CA C 184 189 -117.14 179.80 63.06 27.42 179.80 63.06 27.42 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 4 22 20 19 18 36 29 32 35 46 << 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]: 3112396 3039.449 2.968 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 : 106 106 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 671 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 : 95.9208 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 0.003 0.003 0.60106 1.000 2 Bond angle potential : 44 1 5 3.590 3.590 29.782 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 12 0 1 2.128 2.128 3.3485 1.000 5 Soft-sphere overlap restraints : 671 0 0 0.001 0.001 0.42522E-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 3 3 14.211 74.268 25.334 1.000 14 Sidechain Chi_1 dihedral restraints: 4 0 0 10.022 47.875 0.78357 1.000 15 Sidechain Chi_2 dihedral restraints: 2 0 2 101.937 101.937 6.3004 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 0 7 0.000 0.000 26.126 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 : 671 0 1 1.762 1.762 3.6032 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. report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 5 19 19 17 20 34 30 34 37 47 << end of ENERGY. iupac_m_485_> OD1/2 will be swapped: 157.2914 54 54 iupac_m_484W> Dihedral still outside +-90: 163.3237 openf___224_> Open 1fdx.BL00010001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 openf___224_> Open ${LIB}/atmcls-mf.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3112788 3039.832 2.969 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3112852 3039.895 2.969 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3112910 3039.951 2.969 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3112974 3040.014 2.969 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3113040 3040.078 2.969 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3113104 3040.141 2.969 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3113260 3040.293 2.969 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3113388 3040.418 2.969 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3113682 3040.705 2.969 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3113874 3040.893 2.970 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3114378 3041.385 2.970 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3114634 3041.635 2.970 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3115630 3042.607 2.971 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3116014 3042.982 2.972 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3116590 3043.545 2.972 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3118624 3045.531 2.974 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3119520 3046.406 2.975 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3123972 3050.754 2.979 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3125316 3052.066 2.981 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3134934 3061.459 2.990 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3136918 3063.396 2.992 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3157564 3083.559 3.011 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3160572 3086.496 3.014 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3206538 3131.385 3.058 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3211018 3135.760 3.062 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3312238 3234.607 3.159 openf___224_> Open ${LIB}/dist-mf.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3312634 3234.994 3.159 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3313430 3235.771 3.160 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3314226 3236.549 3.161 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3315414 3237.709 3.162 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3315814 3238.100 3.162 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3316414 3238.686 3.163 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3317314 3239.564 3.164 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3318662 3240.881 3.165 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3318862 3241.076 3.165 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3320886 3243.053 3.167 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3321186 3243.346 3.167 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3324222 3246.311 3.170 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3324670 3246.748 3.171 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3329222 3251.193 3.175 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3329894 3251.850 3.176 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3336722 3258.518 3.182 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3337730 3259.502 3.183 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3347974 3269.506 3.193 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3348574 3270.092 3.193 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3348974 3270.482 3.194 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3350486 3271.959 3.195 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3365850 3286.963 3.210 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3366750 3287.842 3.211 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3367350 3288.428 3.211 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3369618 3290.643 3.214 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3392666 3313.150 3.235 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3394010 3314.463 3.237 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3394910 3315.342 3.238 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3398314 3318.666 3.241 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3432886 3352.428 3.274 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3434902 3354.396 3.276 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3436250 3355.713 3.277 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3441354 3360.697 3.282 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3493210 3411.338 3.331 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3496234 3414.291 3.334 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3498258 3416.268 3.336 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3505914 3423.744 3.344 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3583698 3499.705 3.418 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3588234 3504.135 3.422 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3591270 3507.100 3.425 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3602754 3518.314 3.436 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3719430 3632.256 3.547 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3726234 3638.900 3.554 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3730786 3643.346 3.558 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3748014 3660.170 3.574 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3923030 3831.084 3.741 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3933242 3841.057 3.751 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3940070 3847.725 3.758 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3965910 3872.959 3.782 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 4228434 4129.330 4.033 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 4243746 4144.283 4.047 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 4253990 4154.287 4.057 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 4292750 4192.139 4.094 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 4686534 4576.693 4.469 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 4709502 4599.123 4.491 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 4724866 4614.127 4.506 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 4783006 4670.904 4.561 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5373682 5247.736 5.125 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5408134 5281.381 5.158 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5431182 5303.889 5.180 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5518394 5389.057 5.263 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6404410 6254.307 6.108 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6456094 6304.779 6.157 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6490666 6338.541 6.190 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6621482 6466.291 6.315 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 7950506 7764.166 7.582 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 0 0 0 0 12561 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: ASP:OXT ASP Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 8261182 8067.561 7.878 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 8296990 8102.529 7.913 >> 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 : 106 106 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 5120 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 : 1 9999 NLOGN_USE : 15 CONTACT_SHELL : 15.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : -523.3026 << end of ENERGY. DOPE score : -523.302551 openf___224_> Open 1fdx.IL00000001.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 8004238 7816.639 7.633 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 : 106 106 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 687 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 : 69.7135 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 0.002 0.002 0.15226 1.000 2 Bond angle potential : 44 0 0 1.436 1.436 4.5264 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 12 0 1 2.477 2.477 4.2922 1.000 5 Soft-sphere overlap restraints : 687 0 0 0.001 0.001 0.17692 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 2 2 22.026 22.026 30.162 1.000 14 Sidechain Chi_1 dihedral restraints: 4 0 0 10.777 80.007 1.3153 1.000 15 Sidechain Chi_2 dihedral restraints: 2 0 1 72.055 72.055 3.3036 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 0 7 0.000 0.000 25.267 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 : 687 0 0 1.781 1.781 0.51844 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 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 90 27I 27I CA C 184 189 -129.54 179.80 50.66 22.03 179.80 50.66 22.03 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 4 19 19 19 20 35 30 31 36 50 << end of ENERGY. iupac_m_485_> OD1/2 will be swapped: 157.2914 54 54 iupac_m_484W> Dihedral still outside +-90: 163.3237 openf___224_> Open 1fdx.BL00020001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: ASP:OXT ASP >> 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 : 106 106 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 5208 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 : 1 9999 NLOGN_USE : 15 CONTACT_SHELL : 15.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : -587.0798 << end of ENERGY. DOPE score : -587.079773 openf___224_> Open 1fdx.B99990002.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 7942278 7756.131 7.574 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]: 7944376 7758.180 7.576 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 7973972 7787.082 7.605 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 7974622 7787.717 7.605 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 8004218 7816.619 7.633 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.B99990002.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 8015171 7827.315 7.644 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 8015247 7827.390 7.644 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 8015418 7827.557 7.644 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 8016268 7828.387 7.645 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 8017526 7829.615 7.646 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 8019430 7831.475 7.648 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 8019470 7831.514 7.648 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 8019560 7831.602 7.648 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 8022416 7834.391 7.651 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 8022476 7834.449 7.651 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 8022611 7834.581 7.651 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 8026895 7838.765 7.655 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 8026983 7838.851 7.655 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 8027181 7839.044 7.655 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 8060813 7871.888 7.687 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]: 8006200 7818.555 7.635 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 8007650 7819.971 7.637 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 8010550 7822.803 7.639 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 8071434 7882.260 7.698 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 8071854 7882.670 7.698 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 8072066 7882.877 7.698 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 pick_re_612_> Number of MODEL atoms, selected restraints; 28 106 condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 106 106 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 : 106 106 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 713 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 : 169.4077 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 0.006 0.006 1.5681 1.000 2 Bond angle potential : 44 0 2 2.843 2.843 19.155 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 12 0 0 1.594 1.594 2.5194 1.000 5 Soft-sphere overlap restraints : 713 0 0 0.006 0.006 3.4607 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 2 2 37.284 59.505 57.531 1.000 14 Sidechain Chi_1 dihedral restraints: 4 0 1 14.489 77.860 3.4945 1.000 15 Sidechain Chi_2 dihedral restraints: 2 0 2 86.119 86.119 7.7459 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 0 7 0.000 0.000 29.978 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 : 713 0 9 1.813 1.813 43.955 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 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 90 27I 27I CA C 184 189 -107.13 179.80 73.07 31.77 179.80 73.07 31.77 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 1 2 6 19 26 28 40 42 51 37 41 44 << end of ENERGY. openf___224_> Open 1fdx.IL00000002.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 openf___224_> Open 1fdx.IL00000002.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 8004238 7816.639 7.633 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 : 106 106 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 673 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 : 124.1081 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 0.003 0.003 0.45969 1.000 2 Bond angle potential : 44 0 2 2.473 2.473 15.037 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 12 0 0 2.028 2.028 3.9109 1.000 5 Soft-sphere overlap restraints : 673 0 0 0.003 0.003 0.74142 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 3 3 29.236 106.699 35.960 1.000 14 Sidechain Chi_1 dihedral restraints: 4 0 0 13.146 13.146 2.0085 1.000 15 Sidechain Chi_2 dihedral restraints: 2 0 0 89.099 89.099 1.4449 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 0 8 0.000 0.000 33.192 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 : 673 0 7 1.844 1.844 31.354 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 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 90 27I 27I CA C 184 189 -3.12 0.00 -3.12 -1.36 179.80 177.08 77.00 2 91 7S 7S CA C 50 53 -109.30 179.80 70.90 30.83 179.80 70.90 30.83 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 1 2 6 19 30 29 38 37 49 36 43 50 << end of ENERGY. openf___224_> Open 1fdx.BL00010002.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: ASP:OXT ASP >> 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 : 106 106 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4704 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 : 1 9999 NLOGN_USE : 15 CONTACT_SHELL : 15.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : -358.0874 << end of ENERGY. DOPE score : -358.087372 openf___224_> Open 1fdx.IL00000002.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 8004238 7816.639 7.633 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 : 106 106 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 632 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 : 209.1449 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 0.003 0.003 0.70940 1.000 2 Bond angle potential : 44 4 7 5.040 5.040 51.327 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 12 0 1 2.247 2.247 3.7419 1.000 5 Soft-sphere overlap restraints : 632 0 0 0.006 0.006 2.6374 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 4 4 47.197 86.744 79.831 1.000 14 Sidechain Chi_1 dihedral restraints: 4 0 1 19.893 118.027 6.8314 1.000 15 Sidechain Chi_2 dihedral restraints: 2 0 0 4.671 4.671 -0.99986E-01 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 0 8 0.000 0.000 30.569 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 : 632 0 7 1.881 1.881 33.598 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 38 8C 8C N CA 55 56 127.48 110.93 16.55 5.36 110.93 16.55 5.36 2 44 9I 9I CA N 62 61 131.69 121.39 10.30 5.13 121.39 10.30 5.13 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 90 27I 27I CA C 184 189 -2.32 0.00 -2.32 -1.01 179.80 177.88 77.34 2 91 7S 7S CA C 50 53 -119.61 179.80 60.59 26.34 179.80 60.59 26.34 3 92 26S 26S CA C 178 181 -139.22 179.80 40.98 17.82 179.80 40.98 17.82 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 1 2 7 17 22 32 37 40 51 32 41 45 << end of ENERGY. openf___224_> Open 1fdx.BL00020002.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: ASP:OXT ASP >> 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 : 106 106 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4764 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 : 1 9999 NLOGN_USE : 15 CONTACT_SHELL : 15.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : -353.0020 << end of ENERGY. DOPE score : -353.001984 >> Summary of successfully produced models: Filename molpdf GA341 score ------------------------------------------------------- 1fdx.B99990001.pdb 8490.72363 0.99969 1fdx.B99990002.pdb 2678.72998 0.99999 >> Summary of successfully produced loop models: Filename molpdf DOPE score ------------------------------------------------------- 1fdx.BL00010001.pdb 95.92076 -523.30255 1fdx.BL00020001.pdb 69.71352 -587.07977 1fdx.BL00010002.pdb 124.10812 -358.08737 1fdx.BL00020002.pdb 209.14487 -353.00198 Dynamically allocated memory at finish [B,KiB,MiB]: 7942278 7756.131 7.574 Starting time : 2016/04/05 22:39:35 Closing time : 2016/04/05 22:40:39 Total CPU time [seconds] : 62.46