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 22:39:15 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v16}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v16}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191562 187.072 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192090 187.588 0.183 openf___224_> Open ${MODINSTALL9v16}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240690 235.049 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v16}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253990 248.037 0.242 openf___224_> Open ${MODINSTALL9v16}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v16}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v16}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v16}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open alignment-tiny.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]: 331309 323.544 0.316 Read the alignment from file : alignment-tiny.ali Total number of alignment positions: 106 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 106 1 5fd1 ferredoxin 2 1fdx 10 1 1fdx ferredoxin check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ../atom_files/pdb5fd1.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 364834 356.283 0.348 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 364834 356.283 0.348 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 365005 356.450 0.348 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 365855 357.280 0.349 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 367113 358.509 0.350 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 369017 360.368 0.352 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 369017 360.368 0.352 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 369107 360.456 0.352 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 371963 363.245 0.355 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 371963 363.245 0.355 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 372098 363.377 0.355 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 376382 367.561 0.359 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 376382 367.561 0.359 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 376580 367.754 0.359 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383006 374.029 0.365 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 383006 374.029 0.365 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383303 374.319 0.366 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 392925 383.716 0.375 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 392925 383.716 0.375 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 393375 384.155 0.375 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 392979 383.769 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]: 532231 519.757 0.508 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 533831 521.319 0.509 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 537811 525.206 0.513 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 539811 527.159 0.515 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 542811 530.089 0.518 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 547311 534.483 0.522 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 552883 539.925 0.527 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 555683 542.659 0.530 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 559883 546.761 0.534 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 566183 552.913 0.540 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 568955 555.620 0.543 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 570355 556.987 0.544 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 571768 558.367 0.545 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 579804 566.215 0.553 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 580620 567.012 0.554 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 10 63 62 0 0 20 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 583068 569.402 0.556 patch_______> segment topology patched using RTF: 1 ; ASP ; NTER segments residues atoms bonds angles dihedrals impropers: 1 10 63 62 81 94 20 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 586084 572.348 0.559 patch_______> segment topology patched using RTF: 10 ; LYS ; CTER segments residues atoms bonds angles dihedrals impropers: 1 10 64 63 83 96 21 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 10 64 63 83 96 21 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: 54 10 openf___224_> Open 1fdx.ini wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 693113 676.868 0.661 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 63 83 88 21 Total number of restraints before, now : 0 255 make_re_422_> Number of previous, current restraints : 0 255 make_re_423_> Number of previous, current selected restraints: 0 255 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 697834 681.479 0.666 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 255 263 make_re_423_> Number of previous, current selected restraints: 255 263 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 697850 681.494 0.666 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 9 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 263 272 make_re_423_> Number of previous, current selected restraints: 263 263 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 697850 681.494 0.666 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 272 279 make_re_423_> Number of previous, current selected restraints: 263 270 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 697850 681.494 0.666 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 279 282 make_re_423_> Number of previous, current selected restraints: 270 273 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 697850 681.494 0.666 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 282 283 make_re_423_> Number of previous, current selected restraints: 273 274 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 697850 681.494 0.666 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi4.mdt mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 283 284 make_re_423_> Number of previous, current selected restraints: 274 275 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 716246 699.459 0.683 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 724438 707.459 0.691 make_re_422_> Number of previous, current restraints : 284 314 make_re_423_> Number of previous, current selected restraints: 275 305 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 314 351 make_re_423_> Number of previous, current selected restraints: 305 342 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 351 435 make_re_423_> Number of previous, current selected restraints: 342 426 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 435 438 make_re_423_> Number of previous, current selected restraints: 426 429 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 : 438 438 make_re_423_> Number of previous, current selected restraints: 429 429 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 438 438 make_re_423_> Number of previous, current selected restraints: 429 429 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 438 438 make_re_423_> Number of previous, current selected restraints: 429 429 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 438 438 make_re_423_> Number of previous, current selected restraints: 429 429 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 : 438 438 make_re_423_> Number of previous, current selected restraints: 429 429 rmdupl__427_> 46 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 438 383 openf___224_> Open 1fdx.rsr openf___224_> Open 1fdx.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 597990 583.975 0.570 rdcsr2__307_> Number of restraints read : 383 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 383 383 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]: 598010 583.994 0.570 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 64 64 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 64 340 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 892130 871.221 0.851 pick_re_612_> Number of MODEL atoms, selected restraints; 64 368 pick_re_612_> Number of MODEL atoms, selected restraints; 64 381 pick_re_612_> Number of MODEL atoms, selected restraints; 64 383 iupac_m_485_> OD1/2 will be swapped: 119.9593 1 1 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 10 Number of all, selected real atoms : 64 64 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 383 383 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 64 Dynamic pairs routine : 1, NATM 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 : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 42.2165 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 : 63 0 0 0.002 0.002 0.66934E-01 1.000 2 Bond angle potential : 83 0 0 0.850 0.850 1.0993 1.000 3 Stereochemical cosine torsion poten: 33 0 3 60.478 60.478 16.910 1.000 4 Stereochemical improper torsion pot: 21 0 0 0.638 0.638 0.20225 1.000 5 Soft-sphere overlap restraints : 64 0 0 0.002 0.002 0.18553E-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) : 30 0 0 1.748 1.748 4.7857 1.000 10 Distance restraints 2 (N-O) : 37 0 0 1.063 1.063 2.9428 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: 9 0 0 1.595 1.595 0.27007 1.000 14 Sidechain Chi_1 dihedral restraints: 7 0 0 113.999 113.999 3.2282 1.000 15 Sidechain Chi_2 dihedral restraints: 3 0 0 80.182 80.182 1.3172 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 14.652 14.652 0.32772 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 98.335 98.335 1.1232 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) : 84 0 0 1.180 1.180 3.9286 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 5 1 26.060 131.216 5.7132 1.000 26 Distance restraints 4 (SDCH-SDCH) : 3 0 0 2.607 2.607 0.28297 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: 1518.3190 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 202 2S 3C C N 13 15 50.59 57.40 26.92 0.98 -63.00 153.43 26.71 1 3C 3C N CA 15 16 62.04 36.00 -41.10 2 203 3C 4I C N 19 21 -57.09 -97.30 40.32 1.67 -63.40 173.89 28.72 2 4I 4I N CA 21 22 130.18 127.20 -43.60 3 204 4I 5A C N 27 29 -132.29 -134.00 15.41 0.91 -62.50 171.62 31.86 3 5A 5A N CA 29 30 162.31 147.00 -40.90 4 205 5A 6C C N 32 34 -60.38 -63.00 4.73 0.50 -117.90 -176.88 7.91 4 6C 6C N CA 34 35 -45.04 -41.10 141.10 5 207 7G 8A C N 42 44 -87.04 -68.20 48.80 4.54 -62.50 143.30 22.41 5 8A 8A N CA 44 45 100.28 145.30 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 0 0 4 4 3 4 6 6 6 4 << end of ENERGY. openf___224_> Open 1fdx.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 892150 871.240 0.851 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 64 64 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 64 340 pick_re_612_> Number of MODEL atoms, selected restraints; 64 368 pick_re_612_> Number of MODEL atoms, selected restraints; 64 381 pick_re_612_> Number of MODEL atoms, selected restraints; 64 383 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 10 Number of all, selected real atoms : 64 64 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 383 383 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 79 Dynamic pairs routine : 1, NATM 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 : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 42.9432 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 : 63 0 0 0.003 0.003 0.12888 1.000 2 Bond angle potential : 83 0 0 0.946 0.946 1.3397 1.000 3 Stereochemical cosine torsion poten: 33 0 2 56.662 56.662 15.823 1.000 4 Stereochemical improper torsion pot: 21 0 0 0.885 0.885 0.33023 1.000 5 Soft-sphere overlap restraints : 79 0 0 0.002 0.002 0.52246E-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) : 30 0 0 2.069 2.069 6.5766 1.000 10 Distance restraints 2 (N-O) : 37 0 0 1.342 1.342 4.3262 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: 9 0 0 2.061 2.061 0.45085 1.000 14 Sidechain Chi_1 dihedral restraints: 7 0 0 87.577 87.577 3.4302 1.000 15 Sidechain Chi_2 dihedral restraints: 3 0 0 78.087 78.087 0.60659 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 114.794 114.794 1.0388 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 7.743 7.743 0.26670 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) : 84 0 0 1.166 1.166 3.9743 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 5 1 22.908 133.149 4.3744 1.000 26 Distance restraints 4 (SDCH-SDCH) : 3 0 0 1.965 1.965 0.22409 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: 1351.8540 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 201 1D 2S C N 7 9 -149.58 -136.60 26.56 1.01 -64.10 173.19 18.70 1 2S 2S N CA 9 10 174.38 151.20 -35.00 2 202 2S 3C C N 13 15 -102.39 -117.90 41.16 1.80 -63.00 145.12 20.63 2 3C 3C N CA 15 16 179.23 141.10 -41.10 3 204 4I 5A C N 27 29 50.56 55.40 6.38 0.73 -62.50 135.64 27.55 3 5A 5A N CA 29 30 34.04 38.20 -40.90 4 206 6C 7G C N 38 40 -66.85 -80.20 40.30 1.01 82.20 -163.81 6.72 4 7G 7G N CA 40 41 136.08 174.10 8.50 5 207 7G 8A C N 42 44 -68.21 -68.20 5.45 0.44 -62.50 179.34 29.67 5 8A 8A N CA 44 45 139.85 145.30 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 0 1 4 4 4 3 9 6 4 7 << end of ENERGY. openf___224_> Open 1fdx.B99990002.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 892150 871.240 0.851 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 64 64 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 64 340 pick_re_612_> Number of MODEL atoms, selected restraints; 64 368 pick_re_612_> Number of MODEL atoms, selected restraints; 64 381 pick_re_612_> Number of MODEL atoms, selected restraints; 64 383 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 10 Number of all, selected real atoms : 64 64 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 383 383 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 69 Dynamic pairs routine : 1, NATM 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 : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 42.2491 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 : 63 0 0 0.003 0.003 0.15573 1.000 2 Bond angle potential : 83 0 0 0.927 0.927 1.2594 1.000 3 Stereochemical cosine torsion poten: 33 0 1 51.595 51.595 13.703 1.000 4 Stereochemical improper torsion pot: 21 0 0 0.631 0.631 0.22233 1.000 5 Soft-sphere overlap restraints : 69 0 0 0.001 0.001 0.75603E-02 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) : 30 0 0 1.642 1.642 5.0537 1.000 10 Distance restraints 2 (N-O) : 37 0 0 1.130 1.130 4.0156 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: 9 0 0 2.540 2.540 0.68500 1.000 14 Sidechain Chi_1 dihedral restraints: 7 0 0 96.557 96.557 3.9467 1.000 15 Sidechain Chi_2 dihedral restraints: 3 0 0 8.557 8.557 0.54028 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 89.211 89.211 1.4119 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 39.286 39.286 1.2535 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) : 84 0 0 1.147 1.147 3.2439 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 5 1 26.610 136.538 6.4608 1.000 26 Distance restraints 4 (SDCH-SDCH) : 3 0 0 2.625 2.625 0.28945 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.V99990003 # Heavy relative violation of each residue is written to: 1fdx.V99990003 # 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: 1405.6884 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 201 1D 2S C N 7 9 -62.49 -72.40 10.10 0.66 -64.10 174.56 12.55 1 2S 2S N CA 9 10 150.45 152.40 -35.00 2 202 2S 3C C N 13 15 -67.03 -69.10 2.21 0.16 -63.00 177.91 21.98 2 3C 3C N CA 15 16 141.03 141.80 -41.10 3 203 3C 4I C N 19 21 -53.47 -97.30 44.22 1.85 -63.40 176.96 29.35 3 4I 4I N CA 21 22 133.08 127.20 -43.60 4 204 4I 5A C N 27 29 -111.74 -134.00 23.21 0.56 -62.50 -174.64 32.99 4 5A 5A N CA 29 30 140.41 147.00 -40.90 5 208 8A 9C C N 47 49 -80.06 -69.10 43.35 3.11 -63.00 141.99 16.23 5 9C 9C N CA 49 50 99.86 141.80 -41.10 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 0 0 5 4 0 9 8 3 5 2 << end of ENERGY. openf___224_> Open 1fdx.B99990003.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open $(LIB)/atmcls-melo.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 892556 871.637 0.851 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 892620 871.699 0.851 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 892684 871.762 0.851 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 892812 871.887 0.851 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 893004 872.074 0.852 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 893260 872.324 0.852 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 893644 872.699 0.852 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 894220 873.262 0.853 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 894270 873.311 0.853 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 894328 873.367 0.853 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 895224 874.242 0.854 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 896568 875.555 0.855 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 896634 875.619 0.855 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 898618 877.557 0.857 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 898774 877.709 0.857 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 901782 880.646 0.860 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 902076 880.934 0.860 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 902580 881.426 0.861 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 903576 882.398 0.862 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 908056 886.773 0.866 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 910090 888.760 0.868 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 914542 893.107 0.872 openf___224_> Open $(LIB)/melo1-dist.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 914938 893.494 0.873 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 915734 894.271 0.873 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 916530 895.049 0.874 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 917718 896.209 0.875 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 918118 896.600 0.876 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 918718 897.186 0.876 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 919618 898.064 0.877 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 920966 899.381 0.878 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 922990 901.357 0.880 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 923190 901.553 0.880 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 926226 904.518 0.883 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 926526 904.811 0.884 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 931078 909.256 0.888 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 931526 909.693 0.888 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 938354 916.361 0.895 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 939026 917.018 0.896 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 949270 927.021 0.905 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 950278 928.006 0.906 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 950878 928.592 0.907 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 951278 928.982 0.907 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 966642 943.986 0.922 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 968154 945.463 0.923 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 969054 946.342 0.924 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 969654 946.928 0.925 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 992702 969.436 0.947 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 994970 971.650 0.949 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 996314 972.963 0.950 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 997214 973.842 0.951 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1031786 1007.604 0.984 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1035190 1010.928 0.987 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1037206 1012.896 0.989 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1038554 1014.213 0.990 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1090410 1064.854 1.040 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1095514 1069.838 1.045 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1098538 1072.791 1.048 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1100562 1074.768 1.050 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1178346 1150.729 1.124 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1186002 1158.205 1.131 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1190538 1162.635 1.135 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1193574 1165.600 1.138 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1310250 1279.541 1.250 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]: 1310250 1279.541 1.250 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1311072 1280.344 1.250 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1316390 1285.537 1.255 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1316644 1285.785 1.256 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1321962 1290.979 1.261 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 10 63 62 0 0 20 patch_______> segment topology patched using RTF: 1 ; ASP ; NTER segments residues atoms bonds angles dihedrals impropers: 1 10 63 62 81 94 20 patch_______> segment topology patched using RTF: 10 ; LYS ; CTER segments residues atoms bonds angles dihedrals impropers: 1 10 64 63 83 96 21 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 10 64 63 83 96 21 openf___224_> Open 1fdx.B99990001.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1332915 1301.675 1.271 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1332991 1301.749 1.271 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1333162 1301.916 1.271 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1334012 1302.746 1.272 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1341484 1310.043 1.279 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 # 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: 64 0 25 atoms selected for loop refinement make_re_417_> Restraint type to be calculated: bond r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 26 0 0 0 Total number of restraints before, now : 0 26 make_re_422_> Number of previous, current restraints : 0 26 make_re_423_> Number of previous, current selected restraints: 0 26 make_re_417_> Restraint type to be calculated: angle r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 37 0 0 Total number of restraints before, now : 26 63 make_re_422_> Number of previous, current restraints : 26 63 make_re_423_> Number of previous, current selected restraints: 26 63 make_re_417_> Restraint type to be calculated: improper r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 0 0 10 Total number of restraints before, now : 63 73 make_re_422_> Number of previous, current restraints : 63 73 make_re_423_> Number of previous, current selected restraints: 63 73 make_re_417_> Restraint type to be calculated: dihedral Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1346538 1314.979 1.284 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 0 44 0 Total number of restraints before, now : 73 117 make_re_422_> Number of previous, current restraints : 73 117 make_re_423_> Number of previous, current selected restraints: 73 117 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1346538 1314.979 1.284 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 117 122 make_re_423_> Number of previous, current selected restraints: 117 122 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1346554 1314.994 1.284 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 5 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 122 127 make_re_423_> Number of previous, current selected restraints: 122 122 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1346554 1314.994 1.284 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 127 130 make_re_423_> Number of previous, current selected restraints: 122 125 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1346554 1314.994 1.284 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 130 131 make_re_423_> Number of previous, current selected restraints: 125 126 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1346554 1314.994 1.284 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 131 131 make_re_423_> Number of previous, current selected restraints: 126 126 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1346554 1314.994 1.284 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi4.mdt mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 131 131 make_re_423_> Number of previous, current selected restraints: 126 126 pick_re_612_> Number of MODEL atoms, selected restraints; 25 131 rmdupl__427_> 23 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 131 108 openf___224_> Open 1fdx.lrsr preppdf_457W> Both soft sphere and statistical potential terms selected. Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1640702 1602.248 1.565 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 10 Number of all, selected real atoms : 64 25 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 108 108 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 295 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 : 45.1689 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 : 26 0 0 0.002 0.002 0.26356E-01 1.000 2 Bond angle potential : 37 0 0 0.607 0.607 0.26164 1.000 3 Stereochemical cosine torsion poten: 21 0 2 58.734 58.734 10.690 1.000 4 Stereochemical improper torsion pot: 10 0 0 0.770 0.770 0.14203 1.000 5 Soft-sphere overlap restraints : 295 0 0 0.001 0.001 0.16173E-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: 5 0 0 1.149 1.149 0.77896E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 3 0 0 118.906 118.906 1.0980 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 130.853 130.853 0.67709 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: 5 2 0 23.026 142.632 3.5735 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 : 295 0 6 1.803 1.803 28.606 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 98 4I 5A C N 27 29 -132.34 -134.00 15.43 0.91 -62.50 171.62 31.88 1 5A 5A N CA 29 30 162.34 147.00 -40.90 2 99 5A 6C C N 32 34 -60.42 -63.00 4.69 0.49 -117.90 -176.86 7.91 2 6C 6C N CA 34 35 -45.01 -41.10 141.10 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 0 0 4 4 3 4 6 6 6 4 << end of ENERGY. openf___224_> Open 1fdx.IL00000001.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.IL00000001.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1640722 1602.268 1.565 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 64 25 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. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 10 Number of all, selected real atoms : 64 25 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 108 108 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 268 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 : 20.9771 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 : 26 0 0 0.004 0.004 0.13207 1.000 2 Bond angle potential : 37 0 0 2.312 2.312 4.1260 1.000 3 Stereochemical cosine torsion poten: 21 0 1 50.699 50.699 9.2040 1.000 4 Stereochemical improper torsion pot: 10 0 0 0.983 0.983 0.32941 1.000 5 Soft-sphere overlap restraints : 268 0 0 0.001 0.001 0.21335E-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: 5 0 0 6.155 6.155 2.2358 1.000 14 Sidechain Chi_1 dihedral restraints: 3 0 0 78.183 78.183 0.78197 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 0.176 0.176 -0.27202 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: 5 3 1 27.623 142.417 4.4584 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 : 268 0 2 1.812 1.812 -0.39838E-01 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 95 1D 2S C N 7 9 -115.74 -136.60 26.18 0.81 -64.10 178.03 10.99 1 2S 2S N CA 9 10 135.38 151.20 -35.00 2 98 4I 5A C N 27 29 -100.12 -68.20 32.19 2.86 -62.50 -178.10 31.79 2 5A 5A N CA 29 30 141.13 145.30 -40.90 3 99 5A 6C C N 32 34 -64.54 -63.00 4.20 0.63 -117.90 -178.11 7.82 3 6C 6C N CA 34 35 -45.01 -41.10 141.10 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 1 0 1 3 1 2 4 6 4 3 << end of ENERGY. openf___224_> Open 1fdx.BL00010001.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.IL00000001.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1640722 1602.268 1.565 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 64 25 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. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 10 Number of all, selected real atoms : 64 25 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 108 108 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 274 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 : 23.2193 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 : 26 0 0 0.006 0.006 0.25070 1.000 2 Bond angle potential : 37 0 0 1.514 1.514 1.4915 1.000 3 Stereochemical cosine torsion poten: 21 0 2 55.307 55.307 9.3143 1.000 4 Stereochemical improper torsion pot: 10 0 0 1.255 1.255 0.31536 1.000 5 Soft-sphere overlap restraints : 274 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 5 0 0 2.366 2.366 0.33029 1.000 14 Sidechain Chi_1 dihedral restraints: 3 0 0 91.061 91.061 1.4245 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 0.261 0.261 -0.27030 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: 5 3 1 30.137 142.674 5.1693 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 : 274 0 3 1.717 1.717 5.1935 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 95 1D 2S C N 7 9 -70.65 -72.40 7.15 0.36 -64.10 179.65 13.42 1 2S 2S N CA 9 10 145.47 152.40 -35.00 2 98 4I 5A C N 27 29 -126.78 -134.00 15.75 0.97 -62.50 170.67 31.42 2 5A 5A N CA 29 30 161.00 147.00 -40.90 3 99 5A 6C C N 32 34 -61.80 -63.00 4.09 0.43 -117.90 -177.29 7.88 3 6C 6C N CA 34 35 -45.01 -41.10 141.10 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 0 0 3 2 3 2 3 7 5 6 << end of ENERGY. openf___224_> Open 1fdx.BL00020001.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.B99990002.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1628974 1590.795 1.554 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1629796 1591.598 1.554 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1635114 1596.791 1.559 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1635368 1597.039 1.560 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640686 1602.232 1.565 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 10 63 62 0 0 20 patch_______> segment topology patched using RTF: 1 ; ASP ; NTER segments residues atoms bonds angles dihedrals impropers: 1 10 63 62 81 94 20 patch_______> segment topology patched using RTF: 10 ; LYS ; CTER segments residues atoms bonds angles dihedrals impropers: 1 10 64 63 83 96 21 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 10 64 63 83 96 21 openf___224_> Open 1fdx.B99990002.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1651639 1612.929 1.575 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1651715 1613.003 1.575 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1651886 1613.170 1.575 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1652736 1614.000 1.576 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1660208 1621.297 1.583 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 # 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: 64 0 25 atoms selected for loop refinement make_re_417_> Restraint type to be calculated: bond r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 26 0 0 0 Total number of restraints before, now : 0 26 make_re_422_> Number of previous, current restraints : 0 26 make_re_423_> Number of previous, current selected restraints: 0 26 make_re_417_> Restraint type to be calculated: angle r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 37 0 0 Total number of restraints before, now : 26 63 make_re_422_> Number of previous, current restraints : 26 63 make_re_423_> Number of previous, current selected restraints: 26 63 make_re_417_> Restraint type to be calculated: improper r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 0 0 10 Total number of restraints before, now : 63 73 make_re_422_> Number of previous, current restraints : 63 73 make_re_423_> Number of previous, current selected restraints: 63 73 make_re_417_> Restraint type to be calculated: dihedral r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 0 44 0 Total number of restraints before, now : 73 117 make_re_422_> Number of previous, current restraints : 73 117 make_re_423_> Number of previous, current selected restraints: 73 117 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640686 1602.232 1.565 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 117 122 make_re_423_> Number of previous, current selected restraints: 117 122 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640702 1602.248 1.565 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 5 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 122 127 make_re_423_> Number of previous, current selected restraints: 122 122 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640702 1602.248 1.565 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 127 130 make_re_423_> Number of previous, current selected restraints: 122 125 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640702 1602.248 1.565 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 130 131 make_re_423_> Number of previous, current selected restraints: 125 126 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640702 1602.248 1.565 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 131 131 make_re_423_> Number of previous, current selected restraints: 126 126 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640702 1602.248 1.565 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi4.mdt mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 131 131 make_re_423_> Number of previous, current selected restraints: 126 126 pick_re_612_> Number of MODEL atoms, selected restraints; 25 131 rmdupl__427_> 23 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 131 108 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 : 10 Number of all, selected real atoms : 64 25 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 108 108 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 290 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 : 60.1241 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 : 26 0 0 0.003 0.003 0.49106E-01 1.000 2 Bond angle potential : 37 0 0 1.133 1.133 0.85921 1.000 3 Stereochemical cosine torsion poten: 21 0 2 52.988 52.988 9.7620 1.000 4 Stereochemical improper torsion pot: 10 0 0 1.171 1.171 0.27023 1.000 5 Soft-sphere overlap restraints : 290 0 0 0.001 0.001 0.31556E-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: 5 0 0 2.590 2.590 0.39593 1.000 14 Sidechain Chi_1 dihedral restraints: 3 0 0 123.468 123.468 1.7989 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 3.375 3.375 -0.25234 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: 5 3 1 64.645 131.850 26.616 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 : 290 0 5 1.744 1.744 20.593 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 95 1D 2S C N 7 9 -149.56 -136.60 26.56 1.01 -64.10 173.18 18.70 1 2S 2S N CA 9 10 174.38 151.20 -35.00 2 97 3C 4I C N 19 21 -59.46 -63.40 5.14 0.80 -120.60 -172.54 8.51 2 4I 4I N CA 21 22 -46.91 -43.60 130.30 3 98 4I 5A C N 27 29 50.55 -62.50 135.61 27.55 -62.50 135.61 27.55 3 5A 5A N CA 29 30 34.00 -40.90 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 0 1 4 4 4 3 9 6 4 7 << end of ENERGY. openf___224_> Open 1fdx.IL00000002.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.IL00000002.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1640722 1602.268 1.565 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 64 25 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. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 10 Number of all, selected real atoms : 64 25 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 108 108 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 260 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 : 20.8071 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 : 26 0 0 0.007 0.007 0.34538 1.000 2 Bond angle potential : 37 0 0 1.630 1.630 1.9395 1.000 3 Stereochemical cosine torsion poten: 21 0 1 51.316 51.316 10.351 1.000 4 Stereochemical improper torsion pot: 10 0 0 1.115 1.115 0.28074 1.000 5 Soft-sphere overlap restraints : 260 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 5 0 0 4.537 4.537 1.2145 1.000 14 Sidechain Chi_1 dihedral restraints: 3 0 0 104.789 104.789 0.92442 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 1.725 1.725 -0.26924 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: 5 2 1 30.631 116.973 7.5049 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 : 260 0 0 1.809 1.809 -1.4839 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 95 1D 2S C N 7 9 -131.23 -136.60 15.65 0.88 -64.10 172.68 17.28 1 2S 2S N CA 9 10 165.90 151.20 -35.00 2 98 4I 5A C N 27 29 -130.23 -134.00 21.05 1.10 -62.50 -179.61 27.19 2 5A 5A N CA 29 30 126.29 147.00 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 0 1 3 4 2 1 5 3 3 5 << end of ENERGY. openf___224_> Open 1fdx.BL00010002.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.IL00000002.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1640722 1602.268 1.565 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 64 25 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. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 10 Number of all, selected real atoms : 64 25 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 108 108 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 266 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 : 28.4448 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 : 26 0 0 0.006 0.006 0.23934 1.000 2 Bond angle potential : 37 0 0 2.270 2.270 3.5350 1.000 3 Stereochemical cosine torsion poten: 21 0 0 41.415 41.415 7.0126 1.000 4 Stereochemical improper torsion pot: 10 0 0 1.662 1.662 0.59800 1.000 5 Soft-sphere overlap restraints : 266 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 5 0 0 4.376 4.376 1.1299 1.000 14 Sidechain Chi_1 dihedral restraints: 3 0 0 71.825 71.825 0.82159 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 1.219 1.219 -0.27162 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: 5 3 2 38.507 128.567 13.432 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 : 266 0 0 1.749 1.749 1.9480 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 95 1D 2S C N 7 9 -80.45 -72.40 8.19 0.54 -64.10 171.87 13.49 1 2S 2S N CA 9 10 153.91 152.40 -35.00 2 96 2S 3C C N 13 15 -135.70 -63.00 73.43 11.65 -117.90 172.75 7.05 2 3C 3C N CA 15 16 -30.73 -41.10 141.10 3 98 4I 5A C N 27 29 -90.42 -68.20 42.48 2.73 -62.50 140.40 24.48 3 5A 5A N CA 29 30 -178.49 145.30 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 0 1 2 2 3 1 6 6 3 6 << end of ENERGY. openf___224_> Open 1fdx.BL00020002.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.B99990003.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1628974 1590.795 1.554 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1629796 1591.598 1.554 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1635114 1596.791 1.559 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1635368 1597.039 1.560 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640686 1602.232 1.565 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 10 63 62 0 0 20 patch_______> segment topology patched using RTF: 1 ; ASP ; NTER segments residues atoms bonds angles dihedrals impropers: 1 10 63 62 81 94 20 patch_______> segment topology patched using RTF: 10 ; LYS ; CTER segments residues atoms bonds angles dihedrals impropers: 1 10 64 63 83 96 21 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 10 64 63 83 96 21 openf___224_> Open 1fdx.B99990003.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1651639 1612.929 1.575 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1651715 1613.003 1.575 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1651886 1613.170 1.575 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1652736 1614.000 1.576 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1660208 1621.297 1.583 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 # 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: 64 0 25 atoms selected for loop refinement make_re_417_> Restraint type to be calculated: bond r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 26 0 0 0 Total number of restraints before, now : 0 26 make_re_422_> Number of previous, current restraints : 0 26 make_re_423_> Number of previous, current selected restraints: 0 26 make_re_417_> Restraint type to be calculated: angle r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 37 0 0 Total number of restraints before, now : 26 63 make_re_422_> Number of previous, current restraints : 26 63 make_re_423_> Number of previous, current selected restraints: 26 63 make_re_417_> Restraint type to be calculated: improper r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 0 0 10 Total number of restraints before, now : 63 73 make_re_422_> Number of previous, current restraints : 63 73 make_re_423_> Number of previous, current selected restraints: 63 73 make_re_417_> Restraint type to be calculated: dihedral r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 0 44 0 Total number of restraints before, now : 73 117 make_re_422_> Number of previous, current restraints : 73 117 make_re_423_> Number of previous, current selected restraints: 73 117 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640686 1602.232 1.565 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 117 122 make_re_423_> Number of previous, current selected restraints: 117 122 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640702 1602.248 1.565 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 5 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 122 127 make_re_423_> Number of previous, current selected restraints: 122 122 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640702 1602.248 1.565 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 127 130 make_re_423_> Number of previous, current selected restraints: 122 125 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640702 1602.248 1.565 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 130 131 make_re_423_> Number of previous, current selected restraints: 125 126 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640702 1602.248 1.565 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 131 131 make_re_423_> Number of previous, current selected restraints: 126 126 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1640702 1602.248 1.565 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi4.mdt mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 131 131 make_re_423_> Number of previous, current selected restraints: 126 126 pick_re_612_> Number of MODEL atoms, selected restraints; 25 131 rmdupl__427_> 23 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 131 108 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 : 10 Number of all, selected real atoms : 64 25 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 108 108 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 308 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 : 29.1618 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 : 26 0 0 0.003 0.003 0.73378E-01 1.000 2 Bond angle potential : 37 0 0 0.821 0.821 0.47763 1.000 3 Stereochemical cosine torsion poten: 21 0 0 44.859 44.859 7.6296 1.000 4 Stereochemical improper torsion pot: 10 0 0 0.742 0.742 0.14049 1.000 5 Soft-sphere overlap restraints : 308 0 0 0.000 0.000 0.24183E-02 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: 5 0 0 2.242 2.242 0.29652 1.000 14 Sidechain Chi_1 dihedral restraints: 3 0 0 102.925 102.925 1.4161 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 11.766 11.766 -0.99410E-02 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: 5 2 1 22.916 119.970 4.7195 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 : 308 0 2 1.754 1.754 14.416 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 95 1D 2S C N 7 9 -62.48 -72.40 10.11 0.66 -64.10 174.55 12.55 1 2S 2S N CA 9 10 150.46 152.40 -35.00 2 98 4I 5A C N 27 29 -111.81 -134.00 23.15 0.56 -62.50 -174.62 33.01 2 5A 5A N CA 29 30 140.39 147.00 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 0 0 5 4 0 9 8 3 5 2 << end of ENERGY. openf___224_> Open 1fdx.IL00000003.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.IL00000003.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1640722 1602.268 1.565 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 64 25 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. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 10 Number of all, selected real atoms : 64 25 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 108 108 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 332 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 : 17.8832 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 : 26 0 0 0.005 0.005 0.17370 1.000 2 Bond angle potential : 37 0 0 1.169 1.169 0.96288 1.000 3 Stereochemical cosine torsion poten: 21 0 1 49.405 49.405 7.8742 1.000 4 Stereochemical improper torsion pot: 10 0 0 0.758 0.758 0.14127 1.000 5 Soft-sphere overlap restraints : 332 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 5 0 0 1.709 1.709 0.17225 1.000 14 Sidechain Chi_1 dihedral restraints: 3 0 0 70.174 70.174 0.85732E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 0.542 0.542 -0.27260 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: 5 2 1 18.738 117.085 5.3273 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 : 332 0 0 1.756 1.756 3.4185 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 95 1D 2S C N 7 9 -80.16 -72.40 10.92 0.87 -64.10 -179.57 12.21 1 2S 2S N CA 9 10 144.71 152.40 -35.00 2 98 4I 5A C N 27 29 -67.88 -68.20 18.81 1.51 -62.50 167.47 27.20 2 5A 5A N CA 29 30 126.49 145.30 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 0 0 3 4 3 4 8 6 6 7 << end of ENERGY. openf___224_> Open 1fdx.BL00010003.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.IL00000003.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1640722 1602.268 1.565 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 64 25 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. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 10 Number of all, selected real atoms : 64 25 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 108 108 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 346 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 : 19.7348 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 : 26 0 0 0.006 0.006 0.20409 1.000 2 Bond angle potential : 37 0 0 1.500 1.500 1.4803 1.000 3 Stereochemical cosine torsion poten: 21 0 1 48.334 48.334 7.7374 1.000 4 Stereochemical improper torsion pot: 10 0 0 1.632 1.632 0.67535 1.000 5 Soft-sphere overlap restraints : 346 0 0 0.000 0.000 0.46290E-02 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: 5 0 0 2.727 2.727 0.43874 1.000 14 Sidechain Chi_1 dihedral restraints: 3 0 0 68.987 68.987 1.9380 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 99.205 99.205 0.89368 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: 5 2 0 15.656 114.949 4.5579 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 : 346 0 0 1.772 1.772 1.8048 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 95 1D 2S C N 7 9 -78.64 -72.40 6.24 0.44 -64.10 173.03 13.46 1 2S 2S N CA 9 10 152.58 152.40 -35.00 2 98 4I 5A C N 27 29 -71.40 -68.20 17.39 1.51 -62.50 169.34 27.34 2 5A 5A N CA 29 30 128.20 145.30 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 1 0 4 2 3 6 10 6 5 6 << end of ENERGY. openf___224_> Open 1fdx.BL00020003.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 >> Summary of successfully produced models: Filename molpdf ---------------------------------------- 1fdx.B99990001.pdb 42.21645 1fdx.B99990002.pdb 42.94324 1fdx.B99990003.pdb 42.24908 openf___224_> Open alignment-tiny.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1630956 1592.730 1.555 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1632406 1594.146 1.557 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1635306 1596.979 1.560 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1635726 1597.389 1.560 Read the alignment from file : alignment-tiny.ali Total number of alignment positions: 106 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 106 1 5fd1 ferredoxin Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1637690 1599.307 1.562 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1643008 1604.500 1.567 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1644972 1606.418 1.569 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1650290 1611.611 1.574 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1652254 1613.529 1.576 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1657572 1618.723 1.581 openf___224_> Open .tmp.ali openf___224_> Open .tmp.ali Read the alignment from file : .tmp.ali Total number of alignment positions: 106 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 106 1 5fd1 ferredoxin 2 1fdx_9999 10 1 1fdx.B99990 3 1fdx_9999 10 1 1fdx.B99990 4 1fdx_9999 10 1 1fdx.B99990 compare_343_> >> BEGINNING OF COMMAND openf___224_> Open ../atom_files/pdb5fd1.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1691097 1651.462 1.613 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1691097 1651.462 1.613 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1691268 1651.629 1.613 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1692118 1652.459 1.614 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1693376 1653.688 1.615 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1695280 1655.547 1.617 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1695280 1655.547 1.617 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1695370 1655.635 1.617 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1698226 1658.424 1.620 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1698226 1658.424 1.620 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1698361 1658.556 1.620 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1702645 1662.739 1.624 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1702645 1662.739 1.624 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1702843 1662.933 1.624 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1709269 1669.208 1.630 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1709269 1669.208 1.630 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1709566 1669.498 1.630 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1719188 1678.895 1.640 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1719188 1678.895 1.640 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1719638 1679.334 1.640 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1719242 1678.947 1.640 openf___224_> Open 1fdx.B99990001.pdb Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1719242 1678.947 1.640 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1719332 1679.035 1.640 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1719242 1678.947 1.640 openf___224_> Open 1fdx.B99990002.pdb Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1719242 1678.947 1.640 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1719332 1679.035 1.640 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1719242 1678.947 1.640 openf___224_> Open 1fdx.B99990003.pdb Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1719242 1678.947 1.640 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1719332 1679.035 1.640 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1719242 1678.947 1.640 COMPARISON OF SEVERAL 3D STRUCTURES: # ALGNMT CODE ATOM FILE 1 5fd1 ../atom_files/pdb5fd1.ent 2 1fdx_99990001 1fdx.B99990001.pdb 3 1fdx_99990002 1fdx.B99990002.pdb 4 1fdx_99990003 1fdx.B99990003.pdb Variability at a given position is calculated as: VAR = 1/Nij * sum_ij (feat_i - feat_j) sum runs over all pairs of proteins with residues present. >> Least-squares superposition (FIT) : T Atom types for superposition/RMS (FIT_ATOMS): CA Atom type for position average/variability (VARATOM): CA Position comparison (FIT_ATOMS): Cutoff for RMS calculation: 3.5000 Upper = RMS, Lower = numb equiv positions 5fd1 1fdx_9991fdx_9991fdx_999 5fd1 0.000 2.256 2.553 2.080 1fdx_999 7 0.000 2.109 2.243 1fdx_999 8 8 0.000 2.620 1fdx_999 9 10 5 0.000 Distance comparison (FIT_ATOMS): Cutoff for rms calculation: 3.5000 Upper = Distance RMS, Lower = numb equiv distances 5fd1 1fdx_9991fdx_9991fdx_999 5fd1 0.000 1.321 1.669 1.262 1fdx_999 42 0.000 1.052 1.424 1fdx_999 42 44 0.000 1.295 1fdx_999 45 44 40 0.000 >> Sequence comparison: Diag=numb res, Upper=numb equiv res, Lower = % seq ID 5fd11fdx_9991fdx_9991fdx_999 5fd1 106 1 1 1 1fdx_999 10 10 10 10 1fdx_999 10 100 10 10 1fdx_999 10 100 100 10 >> Dihedral angle comparison: Alph Cutoff for rms comparison: 60.0000 Upper = RMS Alph, Lower = numb of equiv angles 5fd1 1fdx_9991fdx_9991fdx_999 5fd1 0.000 36.560 34.217 42.313 1fdx_999 5 0.000 42.050 40.225 1fdx_999 3 5 0.000 24.879 1fdx_999 5 4 4 0.000 >> Dihedral angle comparison: Phi Cutoff for rms comparison: 60.0000 Upper = RMS Phi , Lower = numb of equiv angles 5fd1 1fdx_9991fdx_9991fdx_999 5fd1 0.000 24.007 27.192 25.301 1fdx_999 6 0.000 13.882 26.364 1fdx_999 7 5 0.000 28.483 1fdx_999 5 8 6 0.000 >> Dihedral angle comparison: Psi Cutoff for rms comparison: 15.0000 Upper = RMS Psi , Lower = numb of equiv angles 5fd1 1fdx_9991fdx_9991fdx_999 5fd1 0.000 4.625 0.000 5.195 1fdx_999 3 0.000 7.009 5.412 1fdx_999 0 2 0.000 1.540 1fdx_999 4 2 1 0.000 >> Dihedral angle comparison: Omeg Cutoff for rms comparison: 60.0000 Upper = RMS Omeg, Lower = numb of equiv angles 5fd1 1fdx_9991fdx_9991fdx_999 5fd1 0.000 8.122 8.883 9.854 1fdx_999 9 0.000 3.291 3.540 1fdx_999 9 9 0.000 2.065 1fdx_999 9 9 9 0.000 >> Dihedral angle comparison: chi1 Cutoff for rms comparison: 60.0000 Upper = RMS chi1, Lower = numb of equiv angles 5fd1 1fdx_9991fdx_9991fdx_999 5fd1 0.000 2.186 15.366 14.434 1fdx_999 1 0.000 0.000 0.159 1fdx_999 4 0 0.000 5.317 1fdx_999 2 1 3 0.000 >> Dihedral angle comparison: chi2 Cutoff for rms comparison: 60.0000 Upper = RMS chi2, Lower = numb of equiv angles 5fd1 1fdx_9991fdx_9991fdx_999 5fd1 0.000 45.985 0.000 38.757 1fdx_999 1 0.000 58.974 31.156 1fdx_999 0 1 0.000 12.469 1fdx_999 1 2 2 0.000 >> Dihedral angle comparison: chi3 Cutoff for rms comparison: 60.0000 Upper = RMS chi3, Lower = numb of equiv angles 5fd1 1fdx_9991fdx_9991fdx_999 5fd1 0.000 40.282 0.000 0.000 1fdx_999 1 0.000 0.000 0.000 1fdx_999 0 0 0.000 0.000 1fdx_999 0 0 0 0.000 >> Dihedral angle comparison: chi4 Cutoff for rms comparison: 60.0000 Upper = RMS chi4, Lower = numb of equiv angles 5fd1 1fdx_9991fdx_9991fdx_999 5fd1 0.000 0.000 24.132 55.652 1fdx_999 0 0.000 0.000 59.054 1fdx_999 1 0 0.000 31.520 1fdx_999 1 1 1 0.000 >> Dihedral angle comparison: chi5 Cutoff for rms comparison: 60.0000 Upper = RMS chi5, Lower = numb of equiv angles 5fd1 1fdx_9991fdx_9991fdx_999 5fd1 0.000 0.000 0.000 0.000 1fdx_999 0 0.000 0.000 0.000 1fdx_999 0 0 0.000 0.000 1fdx_999 0 0 0 0.000 >> Ramachandran mainchain class substitution prot 1 --> prot 2; class on vert --> class on horiz A P B L E U A 3 6 6 2 0 0 P 5 3 5 2 0 0 B 2 6 1 2 0 0 L 0 3 1 1 0 3 E 0 0 0 0 0 0 U 0 0 0 0 0 9 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT A 3 14 17 5.9 27.5 33.3 P 3 12 15 5.9 23.5 29.4 B 1 10 11 2.0 19.6 21.6 L 1 7 8 2.0 13.7 15.7 E 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 8 43 51 15.7 84.3 100.0 -------------------------------------------- U 9 0 9 15.0 0.0 15.0 >> Dihedral class substitution: Alph prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 0 0 3 0 2 0 2 7 6 3 0 4 26 0 4 0 0 0 12 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 0 3 3 0.0 6.2 6.2 2 2 13 15 4.2 27.1 31.2 3 26 4 30 54.2 8.3 62.5 -------------------------------------------- SUMS 28 20 48 58.3 41.7 100.0 -------------------------------------------- 4 12 0 12 20.0 0.0 20.0 >> Dihedral class substitution: Phi prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 17 3 5 0 2 3 1 4 0 3 12 3 6 0 4 0 0 0 6 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 17 8 25 31.5 14.8 46.3 2 1 7 8 1.9 13.0 14.8 3 6 15 21 11.1 27.8 38.9 -------------------------------------------- SUMS 24 30 54 44.4 55.6 100.0 -------------------------------------------- 4 6 0 6 10.0 0.0 10.0 >> Dihedral class substitution: Psi prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 3 2 12 0 2 0 1 4 3 3 7 4 21 0 4 0 0 0 3 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 3 14 17 5.3 24.6 29.8 2 1 7 8 1.8 12.3 14.0 3 21 11 32 36.8 19.3 56.1 -------------------------------------------- SUMS 25 32 57 43.9 56.1 100.0 -------------------------------------------- 4 3 0 3 5.0 0.0 5.0 >> Dihedral class substitution: Omeg prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 54 0 0 3 2 0 0 0 0 3 0 0 0 0 4 0 0 0 3 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 54 3 57 94.7 5.3 100.0 2 0 0 0 0.0 0.0 0.0 3 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 54 3 57 94.7 5.3 100.0 -------------------------------------------- 4 3 0 3 5.0 0.0 5.0 >> Dihedral class substitution: chi1 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 2 8 8 0 2 3 3 5 9 3 3 5 2 0 4 1 0 2 9 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 2 16 18 4.2 33.3 37.5 2 3 17 20 6.2 35.4 41.7 3 2 8 10 4.2 16.7 20.8 -------------------------------------------- SUMS 7 41 48 14.6 85.4 100.0 -------------------------------------------- 4 9 3 12 15.0 5.0 20.0 >> Dihedral class substitution: chi2 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 7 2 0 6 2 3 0 0 6 3 0 0 0 0 4 5 1 0 30 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 7 8 15 29.2 33.3 62.5 2 0 9 9 0.0 37.5 37.5 3 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 7 17 24 29.2 70.8 100.0 -------------------------------------------- 4 30 6 36 50.0 10.0 60.0 >> Dihedral class substitution: chi3 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 1 2 2 0 2 0 0 1 0 3 0 0 0 0 4 0 0 0 54 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 1 4 5 16.7 66.7 83.3 2 0 1 1 0.0 16.7 16.7 3 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 1 5 6 16.7 83.3 100.0 -------------------------------------------- 4 54 0 54 90.0 0.0 90.0 >> Dihedral class substitution: chi4 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 3 0 1 0 2 0 0 0 0 3 2 0 0 0 4 0 0 0 54 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 3 1 4 50.0 16.7 66.7 2 0 0 0 0.0 0.0 0.0 3 0 2 2 0.0 33.3 33.3 -------------------------------------------- SUMS 3 3 6 50.0 50.0 100.0 -------------------------------------------- 4 54 0 54 90.0 0.0 90.0 >> Dihedral class substitution: chi5 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 0 0 0 0 2 0 0 0 0 3 0 0 0 0 4 0 0 0 60 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 0 0 0 0.0 0.0 0.0 2 0 0 0 0.0 0.0 0.0 3 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 0 0 0 0.0 0.0 0.0 -------------------------------------------- 4 60 0 60 100.0 0.0 100.0 compare_344_> << END OF COMMAND Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1721270 1680.928 1.642 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1758064 1716.859 1.677 malign3_328_> Initial framework positions: 106 malign3_330_> Framework, Cycles, RMS_frw(i-1,i): 1 14 0.0000 Least-squares dynamic programming alignment: FIT_ATOMS atoms for alignment : CA Max dist from frw for equivalence : 6.0000 Gap introduction penalty : 0.0000 Gap extension penalty : 3.0000 Numb of residues in framework : 10 malign3_332_> Framework: 1 # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 5fd1 1fdx_9 1fdx_9 1fdx_9 # ============================================= 1 1.338 0.505 A 1 D 1 D 1 D 1 2 1.558 0.308 F 2 S 2 S 2 S 2 3 1.099 0.467 V 3 C 3 C 3 C 3 4 1.678 0.475 V 4 I 4 I 4 I 4 5 1.392 0.505 T 5 A 5 A 5 A 5 6 1.283 0.432 D 6 C 6 C 6 C 6 7 2.031 0.478 N 7 G 7 G 7 G 7 8 1.723 0.385 C 8 A 8 A 8 A 8 9 1.958 0.763 I 9 C 9 C 9 C 9 10 0.993 0.249 * K 10 K 10 K 10 K 10 # ============================================= openf___224_> Open 5fd1_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 106 841 841 openf___224_> Open 1fdx.B99990001_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.B99990002_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.B99990003_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.B99990001.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1639927 1601.491 1.564 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1640003 1601.565 1.564 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1640174 1601.732 1.564 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1641024 1602.562 1.565 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1648496 1609.859 1.572 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1649318 1610.662 1.573 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1654636 1615.855 1.578 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1654890 1616.104 1.578 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1660208 1621.297 1.583 openf___224_> Open 1fdx.BL00010001.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1671161 1631.993 1.594 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1671237 1632.067 1.594 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1671408 1632.234 1.594 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1672258 1633.064 1.595 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1679730 1640.361 1.602 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fdx 2 1fdx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 10 Numb of atoms/sel atoms in MODEL : 64 10 Numb of residues in MODEL2 : 10 Numb of atoms in MODEL2 : 64 Equivalences refinement : F Numb of aligned equiv positions : 10 Numb of aligned equiv distances : 45 RMS before superposition : 0.9245 RMS after superposition : 0.7610 DRMS : 0.3945 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 10 Numb of equiv cutoff distances : 45 Cutoff RMS after superposition : 0.7610 Cutoff DRMS : 0.3945 X_new = Rotation * X + Translation Rotation matrix : 0.9994 -0.0272 -0.0237 0.0278 0.9993 0.0256 0.0229 -0.0262 0.9994 Translation vector: 1.6637 -1.8438 -0.0328 openf___224_> Open 1fdx.BL00010001_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.BL00020001.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1690683 1651.058 1.612 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1690759 1651.132 1.612 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1690930 1651.299 1.613 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1691780 1652.129 1.613 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1699252 1659.426 1.621 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fdx 2 1fdx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 10 Numb of atoms/sel atoms in MODEL : 64 10 Numb of residues in MODEL2 : 10 Numb of atoms in MODEL2 : 64 Equivalences refinement : F Numb of aligned equiv positions : 10 Numb of aligned equiv distances : 45 RMS before superposition : 0.8257 RMS after superposition : 0.7659 DRMS : 0.4526 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 10 Numb of equiv cutoff distances : 45 Cutoff RMS after superposition : 0.7659 Cutoff DRMS : 0.4526 X_new = Rotation * X + Translation Rotation matrix : 0.9970 0.0685 0.0368 -0.0700 0.9967 0.0406 -0.0339 -0.0431 0.9985 Translation vector: -3.0979 0.0586 1.7521 openf___224_> Open 1fdx.BL00020001_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.B99990002.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1690683 1651.058 1.612 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1690759 1651.132 1.612 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1690930 1651.299 1.613 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1691780 1652.129 1.613 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1699252 1659.426 1.621 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1688362 1648.791 1.610 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1693680 1653.984 1.615 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1693934 1654.232 1.615 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1699252 1659.426 1.621 openf___224_> Open 1fdx.BL00010002.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1710205 1670.122 1.631 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1710281 1670.196 1.631 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1710452 1670.363 1.631 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1711302 1671.193 1.632 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1718774 1678.490 1.639 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fdx 2 1fdx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 10 Numb of atoms/sel atoms in MODEL : 64 10 Numb of residues in MODEL2 : 10 Numb of atoms in MODEL2 : 64 Equivalences refinement : F Numb of aligned equiv positions : 10 Numb of aligned equiv distances : 45 RMS before superposition : 0.8205 RMS after superposition : 0.6572 DRMS : 0.5082 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 10 Numb of equiv cutoff distances : 45 Cutoff RMS after superposition : 0.6572 Cutoff DRMS : 0.5082 X_new = Rotation * X + Translation Rotation matrix : 0.9967 0.0768 -0.0259 -0.0797 0.9860 -0.1467 0.0143 0.1483 0.9888 Translation vector: -1.2316 5.1218 -3.2572 openf___224_> Open 1fdx.BL00010002_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.BL00020002.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1690683 1651.058 1.612 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1690759 1651.132 1.612 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1690930 1651.299 1.613 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1691780 1652.129 1.613 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1699252 1659.426 1.621 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fdx 2 1fdx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 10 Numb of atoms/sel atoms in MODEL : 64 10 Numb of residues in MODEL2 : 10 Numb of atoms in MODEL2 : 64 Equivalences refinement : F Numb of aligned equiv positions : 10 Numb of aligned equiv distances : 45 RMS before superposition : 2.1939 RMS after superposition : 1.8000 DRMS : 0.6026 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 9 Numb of equiv cutoff distances : 45 Cutoff RMS after superposition : 1.2014 Cutoff DRMS : 0.6026 X_new = Rotation * X + Translation Rotation matrix : 0.9486 0.2265 -0.2212 -0.3056 0.8378 -0.4525 0.0828 0.4969 0.8639 Translation vector: 1.1703 18.6752 -8.2561 openf___224_> Open 1fdx.BL00020002_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.B99990003.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1690683 1651.058 1.612 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1690759 1651.132 1.612 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1690930 1651.299 1.613 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1691780 1652.129 1.613 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1699252 1659.426 1.621 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1688362 1648.791 1.610 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1693680 1653.984 1.615 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1693934 1654.232 1.615 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1699252 1659.426 1.621 openf___224_> Open 1fdx.BL00010003.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1710205 1670.122 1.631 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1710281 1670.196 1.631 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1710452 1670.363 1.631 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1711302 1671.193 1.632 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1718774 1678.490 1.639 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fdx 2 1fdx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 10 Numb of atoms/sel atoms in MODEL : 64 10 Numb of residues in MODEL2 : 10 Numb of atoms in MODEL2 : 64 Equivalences refinement : F Numb of aligned equiv positions : 10 Numb of aligned equiv distances : 45 RMS before superposition : 0.8599 RMS after superposition : 0.7595 DRMS : 0.5419 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 10 Numb of equiv cutoff distances : 45 Cutoff RMS after superposition : 0.7595 Cutoff DRMS : 0.5419 X_new = Rotation * X + Translation Rotation matrix : 0.9997 -0.0008 0.0225 0.0019 0.9988 -0.0492 -0.0224 0.0492 0.9985 Translation vector: -0.5095 0.7375 -0.2432 openf___224_> Open 1fdx.BL00010003_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 openf___224_> Open 1fdx.BL00020003.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1690683 1651.058 1.612 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1690759 1651.132 1.612 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1690930 1651.299 1.613 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1691780 1652.129 1.613 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1699252 1659.426 1.621 read_mo_297_> Segments, residues, atoms: 1 10 64 read_mo_298_> Segment: 1 1 10 64 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fdx 2 1fdx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 10 Numb of atoms/sel atoms in MODEL : 64 10 Numb of residues in MODEL2 : 10 Numb of atoms in MODEL2 : 64 Equivalences refinement : F Numb of aligned equiv positions : 10 Numb of aligned equiv distances : 45 RMS before superposition : 0.8828 RMS after superposition : 0.7838 DRMS : 0.5629 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 10 Numb of equiv cutoff distances : 45 Cutoff RMS after superposition : 0.7838 Cutoff DRMS : 0.5629 X_new = Rotation * X + Translation Rotation matrix : 0.9999 -0.0085 0.0144 0.0089 0.9994 -0.0337 -0.0141 0.0339 0.9993 Translation vector: -0.2323 0.2657 -0.2155 openf___224_> Open 1fdx.BL00020003_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 10 64 64 >> Summary of successfully produced loop models: Filename molpdf ---------------------------------------- 1fdx.BL00010001.pdb 20.97709 1fdx.BL00020001.pdb 23.21926 1fdx.BL00010002.pdb 20.80711 1fdx.BL00020002.pdb 28.44481 1fdx.BL00010003.pdb 17.88321 1fdx.BL00020003.pdb 19.73479 Dynamically allocated memory at finish [B,KiB,MiB]: 1628974 1590.795 1.554 Starting time : 2016/04/05 22:39:15 Closing time : 2016/04/05 22:39:20 Total CPU time [seconds] : 5.50