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 22:42:21 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 debug_function.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 267058 260.799 0.255 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 268479 262.187 0.256 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269929 263.603 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 302913 295.813 0.289 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 303193 296.087 0.289 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 303453 296.341 0.289 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 303477 296.364 0.289 Read the alignment from file : debug_function.ali Total number of alignment positions: 75 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ctx 71 1 2ctx alpha-cobratoxin 2 2nbt 66 1 2nbt neuronal bungarotoxin 3 1fas 7 1 1fas fasciculin 1 check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ../atom_files/pdb2ctx.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 326502 318.850 0.311 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 326502 318.850 0.311 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 326673 319.017 0.312 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 327523 319.847 0.312 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 328781 321.075 0.314 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 330685 322.935 0.315 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 330685 322.935 0.315 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 330775 323.022 0.315 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 333631 325.812 0.318 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 333631 325.812 0.318 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 333766 325.943 0.318 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 338050 330.127 0.322 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 338050 330.127 0.322 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 338248 330.320 0.323 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 344674 336.596 0.329 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 344674 336.596 0.329 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 344971 336.886 0.329 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 344710 336.631 0.329 openf___224_> Open ../atom_files/2nbt.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 366235 357.651 0.349 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 366235 357.651 0.349 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 366406 357.818 0.349 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 367256 358.648 0.350 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 368514 359.877 0.351 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 370418 361.736 0.353 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 370418 361.736 0.353 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 370508 361.824 0.353 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 373364 364.613 0.356 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 373364 364.613 0.356 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 373499 364.745 0.356 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 377783 368.929 0.360 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 377783 368.929 0.360 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 377981 369.122 0.360 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 384407 375.397 0.367 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 384398 375.389 0.367 check_ali___> Checking pairwise structural superpositions. Equivalent CA pairs with distance difference larger than 6.0 angstroms: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- 1 1 2 1 1 I R 7.634 5 1 2 5 5 I I 11.003 6 1 2 6 6 T S 17.482 7 1 2 7 7 P P 18.661 8 1 2 8 8 D S 13.040 9 1 2 9 9 I S 7.857 15 1 2 13 13 D T 7.571 17 1 2 15 15 P P 7.291 31 1 2 28 29 A K 6.940 32 1 2 29 30 F F 8.486 33 1 2 30 31 C C 6.838 34 1 2 31 32 S S 8.770 35 1 2 32 33 I I 9.240 36 1 2 33 34 R R 6.950 37 1 2 34 35 G G 6.063 50 1 2 47 48 T Q 6.149 51 1 2 48 49 V F 6.114 52 1 2 49 50 K R 8.298 54 1 2 50 52 T N 6.399 56 1 2 52 54 V R 7.067 68 1 2 64 66 P H 7.495 END OF TABLE check_ali___> Checking the sequence-structure alignment. Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE check_a_344_> << END OF COMMAND openf___224_> Open ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 523650 511.377 0.499 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 525250 512.939 0.501 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 529230 516.826 0.505 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 531230 518.779 0.507 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 534230 521.709 0.509 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 538730 526.104 0.514 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 544302 531.545 0.519 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 547102 534.279 0.522 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 551302 538.381 0.526 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 557602 544.533 0.532 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 560374 547.240 0.534 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 561774 548.607 0.536 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 562716 549.527 0.537 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 570066 556.705 0.544 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 570986 557.604 0.545 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 7 56 57 0 0 29 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 573326 559.889 0.547 patch_______> segment topology patched using RTF: 1 ; THR ; NTER segments residues atoms bonds angles dihedrals impropers: 1 7 56 57 76 91 29 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 575862 562.365 0.549 patch_______> segment topology patched using RTF: 7 ; THR ; CTER segments residues atoms bonds angles dihedrals impropers: 1 7 57 58 78 93 30 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 7 57 58 78 93 30 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 2 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 44 13 The following 1 residues contain 6-membered rings with poor geometries after transfer from templates. Rebuilding rings from internal coordinates: openf___224_> Open 1fas.ini wrpdb___568_> Residues, atoms, selected atoms: 7 57 57 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 682891 666.886 0.651 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 58 78 89 30 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]: 686447 670.358 0.655 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 9 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 68 ARG errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 69 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 70 ARG errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 9 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 68 ARG errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 69 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 70 ARG errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 68 ARG errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 69 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 70 ARG errdih__638_> Missing atoms in a dihedral, residue index, residue type: 8 68 ARG errdih__638_> Missing atoms in a dihedral, residue index, residue type: 8 69 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 8 70 ARG getdata_643_> Protein accepted: 2ctx getdata_643_> Protein accepted: 2nbt getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 255 260 make_re_423_> Number of previous, current selected restraints: 255 260 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 686483 670.394 0.655 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 2ctx getdata_643_> Protein accepted: 2nbt getdata_289_> Proteins (all/accepted): 2 2 omgdel__425_> Unselected all O C +N +CA dihedrals: 6 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 260 266 make_re_423_> Number of previous, current selected restraints: 260 260 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 686483 670.394 0.655 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 2ctx getdata_643_> Protein accepted: 2nbt getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 266 273 make_re_423_> Number of previous, current selected restraints: 260 267 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 686483 670.394 0.655 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 2ctx getdata_643_> Protein accepted: 2nbt getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 273 276 make_re_423_> Number of previous, current selected restraints: 267 270 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 686483 670.394 0.655 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 2ctx getdata_643_> Protein accepted: 2nbt getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 276 277 make_re_423_> Number of previous, current selected restraints: 270 271 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 686483 670.394 0.655 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: 2ctx getdata_643_> Protein accepted: 2nbt getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 277 277 make_re_423_> Number of previous, current selected restraints: 271 271 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 702863 686.390 0.670 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 711055 694.390 0.678 make_re_422_> Number of previous, current restraints : 277 291 make_re_423_> Number of previous, current selected restraints: 271 285 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 291 312 make_re_423_> Number of previous, current selected restraints: 285 306 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 312 378 make_re_423_> Number of previous, current selected restraints: 306 372 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 378 379 make_re_423_> Number of previous, current selected restraints: 372 373 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 : 379 379 make_re_423_> Number of previous, current selected restraints: 373 373 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 379 379 make_re_423_> Number of previous, current selected restraints: 373 373 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 379 379 make_re_423_> Number of previous, current selected restraints: 373 373 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 379 379 make_re_423_> Number of previous, current selected restraints: 373 373 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 : 379 379 make_re_423_> Number of previous, current selected restraints: 373 373 rmdupl__427_> 35 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 379 338 openf___224_> Open 1fas.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 879933 859.310 0.839 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 881301 860.646 0.840 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 884037 863.317 0.843 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7 Number of all, selected real atoms : 57 57 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 338 338 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 350 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 : 19677.6328 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 : 58 33 34 0.573 0.573 5230.1 1.000 2 Bond angle potential : 78 25 37 20.168 20.168 668.99 1.000 3 Stereochemical cosine torsion poten: 48 0 2 50.406 50.406 16.377 1.000 4 Stereochemical improper torsion pot: 30 1 5 11.878 11.878 72.976 1.000 5 Soft-sphere overlap restraints : 350 99 111 0.573 0.573 13539. 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 0.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 0.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 0.000 9 Distance restraints 1 (CA-CA) : 14 0 4 3.266 3.556 23.830 1.000 10 Distance restraints 2 (N-O) : 21 0 2 2.424 2.521 31.405 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 0.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 0.000 13 Mainchain Omega dihedral restraints: 6 1 0 34.458 34.458 0.0000 0.000 14 Sidechain Chi_1 dihedral restraints: 7 0 0 11.985 107.520 0.0000 0.000 15 Sidechain Chi_2 dihedral restraints: 3 0 0 5.710 141.135 0.0000 0.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 2.600 106.500 0.0000 0.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 0.000 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 0.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 0.000 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) : 66 0 0 1.101 1.632 71.642 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 0.000 25 Phi/Psi pair of dihedral restraints: 5 0 3 66.083 88.950 21.890 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1 0 0 0.990 3.849 1.6082 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 report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 4 7 1.423 serious non-bonded atom clash: 4 8 1.956 serious non-bonded atom clash: 14 21 2.147 serious non-bonded atom clash: 23 40 2.283 serious non-bonded atom clash: 23 42 1.893 serious non-bonded atom clash: 23 43 1.437 serious non-bonded atom clash: 23 44 1.482 serious non-bonded atom clash: 24 42 1.525 serious non-bonded atom clash: 24 43 0.811 serious non-bonded atom clash: 24 44 2.046 serious non-bonded atom clash: 24 45 2.011 serious non-bonded atom clash: 24 46 1.270 serious non-bonded atom clash: 24 47 2.057 serious non-bonded atom clash: 25 42 1.624 serious non-bonded atom clash: 25 43 1.054 serious non-bonded atom clash: 25 44 2.277 serious non-bonded atom clash: 25 45 1.684 serious non-bonded atom clash: 25 46 1.071 serious non-bonded atom clash: 25 47 1.889 serious non-bonded atom clash: 25 51 2.195 serious non-bonded atom clash: 26 42 1.682 serious non-bonded atom clash: 26 43 2.169 serious non-bonded atom clash: 26 45 1.901 serious non-bonded atom clash: 26 46 2.251 serious non-bonded atom clash: 26 47 1.484 serious non-bonded atom clash: 27 41 2.292 serious non-bonded atom clash: 27 43 1.995 serious non-bonded atom clash: 27 46 1.737 serious non-bonded atom clash: 27 48 2.128 serious non-bonded atom clash: 27 50 1.628 serious non-bonded atom clash: 27 51 1.067 serious non-bonded atom clash: 27 52 0.942 serious non-bonded atom clash: 27 53 1.919 serious non-bonded atom clash: 27 55 2.016 serious non-bonded atom clash: 29 50 2.077 serious non-bonded atom clash: 29 51 0.656 serious non-bonded atom clash: 29 52 1.060 serious non-bonded atom clash: 29 53 1.529 serious non-bonded atom clash: 29 55 0.670 serious non-bonded atom clash: 29 56 1.566 serious non-bonded atom clash: 29 57 1.332 serious non-bonded atom clash: 30 51 1.832 serious non-bonded atom clash: 30 55 1.337 serious non-bonded atom clash: 30 56 1.387 serious non-bonded atom clash: 30 57 1.136 serious non-bonded atom clash: 31 55 2.019 serious non-bonded atom clash: 31 56 1.221 serious non-bonded atom clash: 31 57 1.569 serious non-bonded atom clash: 32 40 1.432 serious non-bonded atom clash: 32 41 1.924 serious non-bonded atom clash: 32 43 1.896 serious non-bonded atom clash: 32 44 0.896 serious non-bonded atom clash: 33 38 1.849 serious non-bonded atom clash: 33 40 1.515 serious non-bonded atom clash: 33 41 2.107 serious non-bonded atom clash: 33 43 2.264 serious non-bonded atom clash: 33 44 1.161 serious non-bonded atom clash: 34 41 1.641 serious non-bonded atom clash: 34 44 1.114 serious non-bonded atom clash: 34 48 2.223 serious non-bonded atom clash: 35 44 1.758 serious non-bonded atom clash: 35 48 2.283 serious non-bonded atom clash: 35 49 2.232 serious non-bonded atom clash: 38 49 1.558 serious non-bonded atom clash: 38 50 2.237 serious non-bonded atom clash: 39 44 2.165 serious non-bonded atom clash: 39 48 1.860 serious non-bonded atom clash: 39 49 1.574 serious non-bonded atom clash: 53 57 1.728 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: 54 6 9 7 8 16 11 14 8 19 16 9 25 18 24 << end of ENERGY. debug_f_621_> Testing the objective function and derivatives code by comparison of numerical and analytical derivatives. Any discrepancies with absolute and relative errors larger than the two cutoffs are written out. Derivatives for individual restraints evaluated : T Absolute error cutoff for whole function : 15.0000 Fractional cutoff for whole function : 0.1000 Absolute error cutoff for restraints : 1.5000 Fractional cutoff for restraints : 0.1000 This test does not work for splines of periodic features! debug_f_617_> End of the function/derivatives test; no discrepancies were found to be above given cutoffs. Dynamically allocated memory at finish [B,KiB,MiB]: 884037 863.317 0.843 Starting time : 2016/04/05 22:42:21 Closing time : 2016/04/05 22:42:22 Total CPU time [seconds] : 0.53