Starting phenix.real_space_refine on Sat Aug 3 04:11:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a64_15205/08_2024/8a64_15205.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a64_15205/08_2024/8a64_15205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a64_15205/08_2024/8a64_15205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a64_15205/08_2024/8a64_15205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a64_15205/08_2024/8a64_15205.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a64_15205/08_2024/8a64_15205.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 4010 2.51 5 N 1357 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6737 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 4639 Classifications: {'peptide': 940} Incomplete info: {'truncation_to_alanine': 819} Link IDs: {'PTRANS': 39, 'TRANS': 900} Unresolved chain link angles: 39 Unresolved non-hydrogen bonds: 2967 Unresolved non-hydrogen angles: 3779 Unresolved non-hydrogen dihedrals: 2486 Unresolved non-hydrogen chiralities: 249 Planarities with less than four sites: {'GLN:plan1': 35, 'ARG:plan': 31, 'TYR:plan': 37, 'ASN:plan1': 51, 'TRP:plan': 12, 'HIS:plan': 14, 'PHE:plan': 34, 'GLU:plan': 64, 'ASP:plan': 75} Unresolved non-hydrogen planarities: 1570 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1032 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 191} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 189} Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 673 Unresolved non-hydrogen angles: 868 Unresolved non-hydrogen dihedrals: 576 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 10, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 353 Chain: "C" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1027 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 189} Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 875 Unresolved non-hydrogen dihedrals: 579 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 10, 'TYR:plan': 9, 'ASN:plan1': 11, 'TRP:plan': 4, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 356 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.68, per 1000 atoms: 0.69 Number of scatterers: 6737 At special positions: 0 Unit cell: (135.708, 87.316, 139.916, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1370 8.00 N 1357 7.00 C 4010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG D 1 " - " ASN B 297 " Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 22 sheets defined 30.2% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.545A pdb=" N SER A 52 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 53 " --> pdb=" O ILE A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 53' Processing helix chain 'A' and resid 57 through 70 Processing helix chain 'A' and resid 76 through 98 removed outlier: 3.937A pdb=" N GLU A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 158 through 167 removed outlier: 4.515A pdb=" N LYS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 206 through 222 Processing helix chain 'A' and resid 223 through 226 Processing helix chain 'A' and resid 247 through 263 Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.403A pdb=" N GLU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 434 through 446 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.814A pdb=" N LEU A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 519 through 523 Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.952A pdb=" N LYS A 528 " --> pdb=" O ALA A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 605 through 622 Processing helix chain 'A' and resid 660 through 665 Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 780 through 788 removed outlier: 4.326A pdb=" N LYS A 786 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL A 787 " --> pdb=" O ASN A 783 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 788 " --> pdb=" O ALA A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 removed outlier: 4.053A pdb=" N ARG A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 860 Processing helix chain 'A' and resid 866 through 868 No H-bonds generated for 'chain 'A' and resid 866 through 868' Processing helix chain 'A' and resid 926 through 943 Processing helix chain 'A' and resid 948 through 966 removed outlier: 3.830A pdb=" N GLU A 954 " --> pdb=" O LYS A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 987 removed outlier: 4.519A pdb=" N ILE A 976 " --> pdb=" O ASP A 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 309 through 315 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 432 through 436 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 117 removed outlier: 6.267A pdb=" N TYR A 114 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 148 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLY A 116 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 179 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASP A 231 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG A 181 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP A 233 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 183 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU A 230 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP A 279 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL A 232 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU A 301 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N MET A 278 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLN A 303 " --> pdb=" O MET A 278 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 300 " --> pdb=" O MET A 342 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY A 344 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 302 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N SER A 346 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR A 341 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE A 400 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE A 343 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TYR A 402 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 345 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU A 113 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N SER A 401 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY A 115 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242 removed outlier: 3.542A pdb=" N VAL A 242 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA4, first strand: chain 'A' and resid 486 through 487 removed outlier: 5.665A pdb=" N LEU A 507 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER A 560 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU A 509 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 517 through 518 removed outlier: 6.721A pdb=" N LEU A 518 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 531 removed outlier: 3.878A pdb=" N GLY A 530 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 638 through 639 Processing sheet with id=AA8, first strand: chain 'A' and resid 649 through 651 Processing sheet with id=AA9, first strand: chain 'A' and resid 657 through 659 Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 removed outlier: 6.755A pdb=" N TYR A 922 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE A 819 " --> pdb=" O TYR A 922 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU A 818 " --> pdb=" O ASN A 892 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASN A 892 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS A 820 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 773 through 775 removed outlier: 3.667A pdb=" N ILE A 810 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N TYR A 897 " --> pdb=" O PHE A 847 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N PHE A 847 " --> pdb=" O TYR A 897 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA A 842 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR A 875 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 844 " --> pdb=" O VAL A 873 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.519A pdb=" N VAL B 302 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 277 through 279 removed outlier: 4.104A pdb=" N TRP B 277 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 319 through 323 Processing sheet with id=AB6, first strand: chain 'B' and resid 347 through 351 removed outlier: 5.551A pdb=" N SER B 364 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL B 412 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N THR B 366 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU B 410 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 368 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER B 408 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS B 370 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 406 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 347 through 351 removed outlier: 5.551A pdb=" N SER B 364 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL B 412 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N THR B 366 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU B 410 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 368 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER B 408 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS B 370 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 406 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 386 through 387 Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 243 removed outlier: 4.047A pdb=" N ASP C 265 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR C 300 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG C 301 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG C 292 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL C 303 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 282 through 284 Processing sheet with id=AC2, first strand: chain 'C' and resid 347 through 351 removed outlier: 5.408A pdb=" N THR C 366 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C 410 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU C 368 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER C 408 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LYS C 370 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU C 406 " --> pdb=" O LYS C 370 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 347 through 351 removed outlier: 5.408A pdb=" N THR C 366 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C 410 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU C 368 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER C 408 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LYS C 370 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU C 406 " --> pdb=" O LYS C 370 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 379 through 380 391 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 1357 1.28 - 1.35: 1347 1.35 - 1.42: 9 1.42 - 1.49: 1372 1.49 - 1.56: 2649 Bond restraints: 6734 Sorted by residual: bond pdb=" C VAL A 901 " pdb=" N PHE A 902 " ideal model delta sigma weight residual 1.329 1.296 0.033 1.36e-02 5.41e+03 5.87e+00 bond pdb=" C THR C 350 " pdb=" N LEU C 351 " ideal model delta sigma weight residual 1.333 1.296 0.036 1.59e-02 3.96e+03 5.14e+00 bond pdb=" N THR B 394 " pdb=" CA THR B 394 " ideal model delta sigma weight residual 1.453 1.474 -0.021 9.20e-03 1.18e+04 5.11e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" CA ASN A 848 " pdb=" C ASN A 848 " ideal model delta sigma weight residual 1.523 1.552 -0.029 1.34e-02 5.57e+03 4.60e+00 ... (remaining 6729 not shown) Histogram of bond angle deviations from ideal: 101.78 - 106.87: 111 106.87 - 111.96: 3446 111.96 - 117.06: 1271 117.06 - 122.15: 3040 122.15 - 127.24: 1507 Bond angle restraints: 9375 Sorted by residual: angle pdb=" CA THR B 299 " pdb=" C THR B 299 " pdb=" O THR B 299 " ideal model delta sigma weight residual 122.31 117.15 5.16 1.31e+00 5.83e-01 1.55e+01 angle pdb=" C VAL A 169 " pdb=" CA VAL A 169 " pdb=" CB VAL A 169 " ideal model delta sigma weight residual 114.00 109.08 4.92 1.31e+00 5.83e-01 1.41e+01 angle pdb=" C LYS A 268 " pdb=" N GLY A 269 " pdb=" CA GLY A 269 " ideal model delta sigma weight residual 122.69 118.98 3.71 1.08e+00 8.57e-01 1.18e+01 angle pdb=" N GLY A 269 " pdb=" CA GLY A 269 " pdb=" C GLY A 269 " ideal model delta sigma weight residual 112.10 117.66 -5.56 1.82e+00 3.02e-01 9.34e+00 angle pdb=" N GLU A 102 " pdb=" CA GLU A 102 " pdb=" C GLU A 102 " ideal model delta sigma weight residual 110.28 105.92 4.36 1.48e+00 4.57e-01 8.67e+00 ... (remaining 9370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.51: 3955 22.51 - 45.01: 1 45.01 - 67.52: 3 67.52 - 90.02: 6 90.02 - 112.53: 4 Dihedral angle restraints: 3969 sinusoidal: 64 harmonic: 3905 Sorted by residual: dihedral pdb=" CA SER B 337 " pdb=" C SER B 337 " pdb=" N LYS B 338 " pdb=" CA LYS B 338 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C3 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 47.62 -64.91 112.53 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 288.71 176.83 111.88 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 3966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1208 0.103 - 0.206: 83 0.206 - 0.310: 1 0.310 - 0.413: 0 0.413 - 0.516: 1 Chirality restraints: 1293 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 297 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.92 0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.47 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1290 not shown) Planarity restraints: 1355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 297 " 0.127 2.00e-02 2.50e+03 1.74e-01 3.80e+02 pdb=" CG ASN B 297 " -0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN B 297 " 0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN B 297 " -0.299 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 100 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.88e+00 pdb=" C ILE A 100 " -0.042 2.00e-02 2.50e+03 pdb=" O ILE A 100 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO A 101 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 297 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C ASN B 297 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN B 297 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 298 " -0.010 2.00e-02 2.50e+03 ... (remaining 1352 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 225 2.67 - 3.23: 7294 3.23 - 3.78: 10133 3.78 - 4.34: 11868 4.34 - 4.90: 17827 Nonbonded interactions: 47347 Sorted by model distance: nonbonded pdb=" O LEU A 509 " pdb=" N SER A 560 " model vdw 2.112 3.120 nonbonded pdb=" O ILE A 261 " pdb=" N ILE A 265 " model vdw 2.132 3.120 nonbonded pdb=" O ILE A 343 " pdb=" N PHE A 400 " model vdw 2.132 3.120 nonbonded pdb=" O LEU A 485 " pdb=" N ASP A 508 " model vdw 2.144 3.120 nonbonded pdb=" N ASP C 399 " pdb=" O SER C 403 " model vdw 2.190 3.120 ... (remaining 47342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 237 through 280 and (name N or name CA or name C or name \ O or name CB )) or (resid 281 through 315 and (name N or name CA or name C or na \ me O or name CB )) or resid 316 through 443)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.180 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 6734 Z= 0.575 Angle : 0.863 8.616 9375 Z= 0.574 Chirality : 0.056 0.516 1293 Planarity : 0.006 0.024 1354 Dihedral : 10.170 112.526 1415 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.22), residues: 1348 helix: -1.30 (0.27), residues: 306 sheet: -1.02 (0.28), residues: 316 loop : -0.80 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.795 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0693 time to fit residues: 3.6485 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.0980 chunk 54 optimal weight: 50.0000 chunk 105 optimal weight: 30.0000 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6734 Z= 0.168 Angle : 0.545 9.834 9375 Z= 0.310 Chirality : 0.045 0.409 1293 Planarity : 0.003 0.013 1354 Dihedral : 7.480 68.124 1412 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1348 helix: 0.25 (0.29), residues: 323 sheet: -1.09 (0.28), residues: 326 loop : -0.27 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.721 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0645 time to fit residues: 3.5045 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 50.0000 chunk 101 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 131 optimal weight: 50.0000 chunk 108 optimal weight: 50.0000 chunk 120 optimal weight: 50.0000 chunk 41 optimal weight: 30.0000 chunk 97 optimal weight: 50.0000 overall best weight: 11.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6734 Z= 0.275 Angle : 0.626 9.151 9375 Z= 0.361 Chirality : 0.045 0.359 1293 Planarity : 0.003 0.025 1354 Dihedral : 6.365 41.384 1412 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1348 helix: 0.58 (0.29), residues: 325 sheet: -1.47 (0.29), residues: 308 loop : -0.48 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.733 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0615 time to fit residues: 3.4083 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 50.0000 chunk 91 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 50.0000 chunk 58 optimal weight: 50.0000 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 40.0000 chunk 129 optimal weight: 0.0270 chunk 115 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 6734 Z= 0.138 Angle : 0.466 11.035 9375 Z= 0.265 Chirality : 0.045 0.482 1293 Planarity : 0.002 0.009 1354 Dihedral : 5.463 48.676 1412 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.24), residues: 1348 helix: 1.10 (0.30), residues: 338 sheet: -1.50 (0.29), residues: 297 loop : -0.42 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.687 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0600 time to fit residues: 3.3365 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 8.9990 chunk 1 optimal weight: 50.0000 chunk 96 optimal weight: 40.0000 chunk 53 optimal weight: 50.0000 chunk 110 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 66 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 32 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 6734 Z= 0.314 Angle : 0.609 10.615 9375 Z= 0.364 Chirality : 0.045 0.469 1293 Planarity : 0.003 0.017 1354 Dihedral : 6.140 39.585 1412 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.24), residues: 1348 helix: 1.10 (0.30), residues: 319 sheet: -1.95 (0.29), residues: 288 loop : -0.75 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.719 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0568 time to fit residues: 3.2074 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 30.0000 chunk 25 optimal weight: 50.0000 chunk 76 optimal weight: 50.0000 chunk 31 optimal weight: 8.9990 chunk 129 optimal weight: 0.5980 chunk 107 optimal weight: 50.0000 chunk 60 optimal weight: 50.0000 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 overall best weight: 8.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6734 Z= 0.199 Angle : 0.497 8.209 9375 Z= 0.288 Chirality : 0.044 0.345 1293 Planarity : 0.002 0.010 1354 Dihedral : 5.544 48.837 1412 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.24), residues: 1348 helix: 1.32 (0.31), residues: 327 sheet: -1.97 (0.30), residues: 269 loop : -0.75 (0.25), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.725 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0622 time to fit residues: 3.4021 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 50.0000 chunk 109 optimal weight: 30.0000 chunk 72 optimal weight: 0.0270 chunk 129 optimal weight: 0.0980 chunk 80 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 59 optimal weight: 20.0000 chunk 79 optimal weight: 50.0000 chunk 51 optimal weight: 7.9990 overall best weight: 4.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 6734 Z= 0.128 Angle : 0.430 11.235 9375 Z= 0.246 Chirality : 0.044 0.412 1293 Planarity : 0.002 0.010 1354 Dihedral : 4.998 49.515 1412 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1348 helix: 1.61 (0.30), residues: 348 sheet: -1.98 (0.30), residues: 275 loop : -0.45 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.778 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0635 time to fit residues: 3.4912 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 50.0000 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 50.0000 chunk 82 optimal weight: 50.0000 chunk 87 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 112 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 6734 Z= 0.175 Angle : 0.460 9.701 9375 Z= 0.266 Chirality : 0.044 0.397 1293 Planarity : 0.002 0.010 1354 Dihedral : 5.169 44.694 1412 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1348 helix: 1.84 (0.30), residues: 334 sheet: -2.13 (0.29), residues: 286 loop : -0.48 (0.26), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 121 PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.771 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0667 time to fit residues: 3.6239 Evaluate side-chains 20 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6212 > 50: distance: 27 - 95: 30.939 distance: 30 - 92: 28.132 distance: 37 - 85: 35.780 distance: 40 - 82: 29.603 distance: 49 - 52: 30.958 distance: 52 - 53: 6.396 distance: 53 - 54: 38.775 distance: 53 - 56: 13.160 distance: 54 - 55: 28.606 distance: 54 - 57: 37.785 distance: 57 - 58: 3.433 distance: 58 - 59: 26.744 distance: 58 - 61: 47.257 distance: 59 - 60: 13.442 distance: 59 - 62: 39.211 distance: 62 - 63: 15.547 distance: 63 - 64: 40.139 distance: 63 - 66: 56.030 distance: 64 - 65: 16.859 distance: 64 - 67: 7.417 distance: 67 - 68: 44.024 distance: 68 - 69: 46.527 distance: 68 - 71: 32.718 distance: 69 - 70: 32.550 distance: 69 - 72: 7.713 distance: 72 - 73: 14.567 distance: 73 - 74: 52.767 distance: 73 - 76: 38.528 distance: 74 - 75: 51.841 distance: 78 - 79: 38.289 distance: 78 - 81: 32.362 distance: 79 - 80: 40.237 distance: 79 - 82: 25.460 distance: 82 - 83: 22.699 distance: 83 - 84: 4.540 distance: 83 - 86: 25.567 distance: 84 - 85: 7.682 distance: 84 - 87: 28.748 distance: 87 - 88: 40.538 distance: 88 - 89: 9.526 distance: 88 - 91: 8.045 distance: 89 - 90: 68.961 distance: 89 - 92: 42.380 distance: 92 - 93: 8.751 distance: 93 - 96: 13.173 distance: 94 - 95: 27.711 distance: 94 - 97: 24.222 distance: 97 - 98: 32.466 distance: 98 - 99: 27.886 distance: 98 - 101: 23.244 distance: 99 - 100: 39.038 distance: 99 - 102: 30.336