Starting phenix.real_space_refine on Fri Sep 27 18:39:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/09_2024/3jbr_6475.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/09_2024/3jbr_6475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/09_2024/3jbr_6475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/09_2024/3jbr_6475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/09_2024/3jbr_6475.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbr_6475/09_2024/3jbr_6475.cif" } resolution = 4.2 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= -0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 52 5.16 5 C 10360 2.51 5 N 2910 2.21 5 O 3144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16467 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 6977 Classifications: {'peptide': 1099} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 539} Link IDs: {'CIS': 12, 'PTRANS': 31, 'TRANS': 1055} Chain breaks: 7 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 2014 Unresolved non-hydrogen angles: 2601 Unresolved non-hydrogen dihedrals: 1699 Unresolved non-hydrogen chiralities: 204 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 12, 'TYR:plan': 27, 'ASN:plan1': 29, 'TRP:plan': 10, 'ASP:plan': 21, 'PHE:plan': 39, 'GLU:plan': 34, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 1080 Chain: "A" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 624 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 112} Link IDs: {'CIS': 1, 'TRANS': 123} Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2210 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 263} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 688 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 537 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 6, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 12, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 202 Chain: "F" Number of atoms: 4194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4194 Classifications: {'peptide': 574} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 112} Link IDs: {'CIS': 6, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 543} Chain breaks: 3 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 433 Unresolved non-hydrogen angles: 570 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 8, 'ASN:plan1': 7, 'TYR:plan': 14, 'UNK:plan-1': 16, 'TRP:plan': 1, 'ASP:plan': 9, 'ARG:plan': 3, 'PHE:plan': 2, 'GLU:plan': 11, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 289 Chain: "F" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 1541 Classifications: {'peptide': 298} Incomplete info: {'backbone_only': 17, 'truncation_to_alanine': 250} Link IDs: {'CIS': 3, 'PTRANS': 5, 'TRANS': 289} Chain breaks: 14 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 920 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'UNK:plan-1': 226, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 325 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 232 Unusual residues: {'BMA': 2, 'NAG': 15} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 10.26, per 1000 atoms: 0.62 Number of scatterers: 16467 At special positions: 0 Unit cell: (188.76, 163.68, 149.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 52 16.00 O 3144 8.00 N 2910 7.00 C 10360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1062 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 TRANS " UNK A1396 " - " GLY A1395 " Time building additional restraints: 4.44 Conformation dependent library (CDL) restraints added in 2.1 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 11 sheets defined 71.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 39 through 49 removed outlier: 4.075A pdb=" N ALA A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 72 removed outlier: 4.205A pdb=" N THR A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 106 removed outlier: 3.956A pdb=" N LEU A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 115 through 139 removed outlier: 3.991A pdb=" N ALA A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.929A pdb=" N VAL A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.679A pdb=" N LYS A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 215 Processing helix chain 'A' and resid 216 through 226 removed outlier: 4.093A pdb=" N LYS A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 226 " --> pdb=" O MET A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.855A pdb=" N VAL A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 344 removed outlier: 3.962A pdb=" N TYR A 313 " --> pdb=" O TRP A 309 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 372 Processing helix chain 'A' and resid 426 through 432 Processing helix chain 'A' and resid 437 through 460 removed outlier: 3.636A pdb=" N ALA A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Proline residue: A 457 - end of helix Processing helix chain 'A' and resid 473 through 497 removed outlier: 3.746A pdb=" N ILE A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 503 removed outlier: 3.583A pdb=" N CYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 517 removed outlier: 3.645A pdb=" N GLY A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.995A pdb=" N ARG A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.943A pdb=" N TYR A 541 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 580 removed outlier: 3.871A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 Processing helix chain 'A' and resid 615 through 627 removed outlier: 4.016A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 637 Processing helix chain 'A' and resid 638 through 669 removed outlier: 4.121A pdb=" N VAL A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 808 through 829 Proline residue: A 821 - end of helix Processing helix chain 'A' and resid 830 through 837 removed outlier: 6.325A pdb=" N GLY A 833 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE A 835 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 862 removed outlier: 3.733A pdb=" N SER A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 872 Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.572A pdb=" N VAL A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 885 " --> pdb=" O ILE A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 902 removed outlier: 3.802A pdb=" N VAL A 901 " --> pdb=" O VAL A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 912 through 928 removed outlier: 3.544A pdb=" N HIS A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 951 removed outlier: 3.794A pdb=" N LEU A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1015 through 1025 removed outlier: 3.845A pdb=" N LEU A1019 " --> pdb=" O GLY A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1040 No H-bonds generated for 'chain 'A' and resid 1038 through 1040' Processing helix chain 'A' and resid 1041 through 1076 removed outlier: 4.359A pdb=" N PHE A1045 " --> pdb=" O MET A1041 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N MET A1057 " --> pdb=" O ALA A1053 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A1064 " --> pdb=" O PHE A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1118 through 1137 removed outlier: 4.208A pdb=" N TYR A1122 " --> pdb=" O SER A1118 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A1123 " --> pdb=" O TYR A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1170 Processing helix chain 'A' and resid 1181 through 1202 Processing helix chain 'A' and resid 1203 through 1204 No H-bonds generated for 'chain 'A' and resid 1203 through 1204' Processing helix chain 'A' and resid 1229 through 1229 No H-bonds generated for 'chain 'A' and resid 1229 through 1229' Processing helix chain 'A' and resid 1230 through 1241 removed outlier: 4.223A pdb=" N PHE A1234 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A1238 " --> pdb=" O PHE A1234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A1239 " --> pdb=" O PHE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1250 removed outlier: 3.698A pdb=" N LEU A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1265 removed outlier: 3.543A pdb=" N LEU A1257 " --> pdb=" O VAL A1253 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A1265 " --> pdb=" O ILE A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1287 removed outlier: 3.686A pdb=" N ALA A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A1272 " --> pdb=" O PRO A1268 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A1273 " --> pdb=" O TYR A1269 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A1278 " --> pdb=" O ILE A1274 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A1283 " --> pdb=" O PHE A1279 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN A1287 " --> pdb=" O VAL A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1319 removed outlier: 3.864A pdb=" N CYS A1319 " --> pdb=" O LEU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1322 No H-bonds generated for 'chain 'A' and resid 1320 through 1322' Processing helix chain 'A' and resid 1324 through 1333 removed outlier: 3.869A pdb=" N ILE A1328 " --> pdb=" O ALA A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1383 removed outlier: 4.275A pdb=" N PHE A1361 " --> pdb=" O ALA A1357 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A1366 " --> pdb=" O ILE A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1395 removed outlier: 5.146A pdb=" N ARG A1389 " --> pdb=" O ASP A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1411 removed outlier: 3.808A pdb=" N UNK A1404 " --> pdb=" O UNK A1400 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N UNK A1411 " --> pdb=" O UNK A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1423 through 1434 removed outlier: 4.066A pdb=" N UNK A1432 " --> pdb=" O UNK A1428 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N UNK A1433 " --> pdb=" O UNK A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1454 Processing helix chain 'A' and resid 1459 through 1475 removed outlier: 3.983A pdb=" N UNK A1473 " --> pdb=" O UNK A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1484 removed outlier: 3.594A pdb=" N UNK A1483 " --> pdb=" O UNK A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1498 removed outlier: 3.691A pdb=" N UNK A1498 " --> pdb=" O UNK A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1520 removed outlier: 3.899A pdb=" N UNK A1509 " --> pdb=" O UNK A1505 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNK A1512 " --> pdb=" O UNK A1508 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N UNK A1516 " --> pdb=" O UNK A1512 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N UNK A1518 " --> pdb=" O UNK A1514 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N UNK A1519 " --> pdb=" O UNK A1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 57 removed outlier: 3.631A pdb=" N ARG B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 120 through 135 Processing helix chain 'B' and resid 239 through 257 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 295 through 310 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 325 through 332 removed outlier: 4.204A pdb=" N LYS B 331 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 removed outlier: 3.589A pdb=" N LEU B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 377 removed outlier: 3.679A pdb=" N CYS B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 removed outlier: 3.661A pdb=" N PHE B 383 " --> pdb=" O PRO B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 411 removed outlier: 3.641A pdb=" N ALA B 395 " --> pdb=" O GLN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'E' and resid 6 through 29 removed outlier: 3.586A pdb=" N VAL E 11 " --> pdb=" O PRO E 7 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE E 14 " --> pdb=" O ARG E 10 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS E 15 " --> pdb=" O VAL E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 128 Processing helix chain 'E' and resid 131 through 166 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 180 through 204 removed outlier: 3.790A pdb=" N CYS E 184 " --> pdb=" O TRP E 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 54 No H-bonds generated for 'chain 'F' and resid 52 through 54' Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.915A pdb=" N LEU F 59 " --> pdb=" O UNK F 55 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL F 60 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP F 61 " --> pdb=" O HIS F 57 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 112 removed outlier: 3.596A pdb=" N ARG F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 201 removed outlier: 3.564A pdb=" N LEU F 182 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU F 191 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 removed outlier: 3.638A pdb=" N ILE F 247 " --> pdb=" O ARG F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 285 removed outlier: 4.387A pdb=" N GLU F 283 " --> pdb=" O SER F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.669A pdb=" N ASN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 348 removed outlier: 3.665A pdb=" N GLU F 344 " --> pdb=" O SER F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 379 Processing helix chain 'F' and resid 398 through 408 removed outlier: 3.755A pdb=" N CYS F 406 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 429 removed outlier: 3.581A pdb=" N THR F 425 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU F 427 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR F 428 " --> pdb=" O ASN F 424 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU F 429 " --> pdb=" O THR F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 432 No H-bonds generated for 'chain 'F' and resid 430 through 432' Processing helix chain 'F' and resid 433 through 438 Processing helix chain 'F' and resid 485 through 491 Processing helix chain 'F' and resid 562 through 567 removed outlier: 3.522A pdb=" N GLU F 567 " --> pdb=" O PHE F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 581 Processing helix chain 'F' and resid 639 through 652 Processing helix chain 'F' and resid 663 through 677 Processing helix chain 'F' and resid 681 through 697 Processing helix chain 'F' and resid 732 through 751 Processing helix chain 'F' and resid 752 through 765 removed outlier: 3.794A pdb=" N UNK F 765 " --> pdb=" O UNK F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 778 through 799 removed outlier: 3.909A pdb=" N UNK F 799 " --> pdb=" O UNK F 795 " (cutoff:3.500A) Processing helix chain 'F' and resid 859 through 867 Processing helix chain 'F' and resid 903 through 912 Processing helix chain 'F' and resid 931 through 938 Processing helix chain 'F' and resid 978 through 989 Processing sheet with id=A, first strand: chain 'A' and resid 974 through 975 Processing sheet with id=B, first strand: chain 'B' and resid 116 through 119 removed outlier: 3.610A pdb=" N GLU B 97 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG B 107 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL B 95 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B 63 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.612A pdb=" N VAL B 230 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL B 385 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=E, first strand: chain 'F' and resid 44 through 45 Processing sheet with id=F, first strand: chain 'F' and resid 166 through 167 removed outlier: 3.735A pdb=" N TYR F 219 " --> pdb=" O GLN F 208 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN F 208 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP F 207 " --> pdb=" O LYS F 482 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'F' and resid 300 through 302 removed outlier: 7.656A pdb=" N MET F 256 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS F 358 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N PHE F 387 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'F' and resid 500 through 501 removed outlier: 4.513A pdb=" N LYS F 500 " --> pdb=" O LEU F 624 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 624 " --> pdb=" O LYS F 500 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'F' and resid 594 through 596 Processing sheet with id=J, first strand: chain 'F' and resid 806 through 807 Processing sheet with id=K, first strand: chain 'F' and resid 827 through 832 removed outlier: 3.686A pdb=" N UNK F 832 " --> pdb=" O UNK F 839 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 3000 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: 5.48 Time building geometry restraints manager: 5.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3263 1.32 - 1.45: 4080 1.45 - 1.57: 9234 1.57 - 1.69: 0 1.69 - 1.82: 84 Bond restraints: 16661 Sorted by residual: bond pdb=" N PRO F 627 " pdb=" CD PRO F 627 " ideal model delta sigma weight residual 1.473 1.545 -0.072 1.40e-02 5.10e+03 2.61e+01 bond pdb=" CA ILE A 229 " pdb=" CB ILE A 229 " ideal model delta sigma weight residual 1.548 1.512 0.036 1.13e-02 7.83e+03 1.02e+01 bond pdb=" CA ILE A 213 " pdb=" CB ILE A 213 " ideal model delta sigma weight residual 1.540 1.499 0.041 1.29e-02 6.01e+03 9.90e+00 bond pdb=" CA PRO F 171 " pdb=" CB PRO F 171 " ideal model delta sigma weight residual 1.532 1.491 0.041 1.33e-02 5.65e+03 9.47e+00 bond pdb=" CA VAL A 203 " pdb=" CB VAL A 203 " ideal model delta sigma weight residual 1.540 1.504 0.036 1.17e-02 7.31e+03 9.31e+00 ... (remaining 16656 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 22078 3.11 - 6.21: 614 6.21 - 9.32: 96 9.32 - 12.42: 5 12.42 - 15.53: 3 Bond angle restraints: 22796 Sorted by residual: angle pdb=" N PRO A 987 " pdb=" CA PRO A 987 " pdb=" CB PRO A 987 " ideal model delta sigma weight residual 102.35 110.96 -8.61 7.10e-01 1.98e+00 1.47e+02 angle pdb=" C CYS F 509 " pdb=" N PRO F 510 " pdb=" CA PRO F 510 " ideal model delta sigma weight residual 119.84 130.15 -10.31 1.25e+00 6.40e-01 6.81e+01 angle pdb=" N PRO F1059 " pdb=" CA PRO F1059 " pdb=" CB PRO F1059 " ideal model delta sigma weight residual 103.31 110.44 -7.13 8.90e-01 1.26e+00 6.43e+01 angle pdb=" N PRO F 171 " pdb=" CA PRO F 171 " pdb=" CB PRO F 171 " ideal model delta sigma weight residual 103.27 110.44 -7.17 9.00e-01 1.23e+00 6.34e+01 angle pdb=" N PRO F1044 " pdb=" CA PRO F1044 " pdb=" CB PRO F1044 " ideal model delta sigma weight residual 103.27 110.28 -7.01 9.00e-01 1.23e+00 6.07e+01 ... (remaining 22791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.37: 9901 25.37 - 50.73: 88 50.73 - 76.10: 28 76.10 - 101.47: 16 101.47 - 126.83: 7 Dihedral angle restraints: 10040 sinusoidal: 2752 harmonic: 7288 Sorted by residual: dihedral pdb=" CA ARG F 243 " pdb=" C ARG F 243 " pdb=" N PRO F 244 " pdb=" CA PRO F 244 " ideal model delta harmonic sigma weight residual 180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LEU F1034 " pdb=" C LEU F1034 " pdb=" N ILE F1035 " pdb=" CA ILE F1035 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA TYR A 621 " pdb=" C TYR A 621 " pdb=" N ASN A 622 " pdb=" CA ASN A 622 " ideal model delta harmonic sigma weight residual 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 10037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2341 0.066 - 0.132: 448 0.132 - 0.199: 37 0.199 - 0.265: 20 0.265 - 0.331: 11 Chirality restraints: 2857 Sorted by residual: chirality pdb=" CA PRO A 244 " pdb=" N PRO A 244 " pdb=" C PRO A 244 " pdb=" CB PRO A 244 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA PRO A 266 " pdb=" N PRO A 266 " pdb=" C PRO A 266 " pdb=" CB PRO A 266 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA PRO F 74 " pdb=" N PRO F 74 " pdb=" C PRO F 74 " pdb=" CB PRO F 74 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2854 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 509 " -0.042 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO F 510 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO F 510 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 510 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 300 " 0.014 2.00e-02 2.50e+03 1.22e-02 3.70e+00 pdb=" CG TRP A 300 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 300 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 300 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 300 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 300 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 300 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 300 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 300 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 300 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN F 530 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO F 531 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO F 531 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 531 " -0.028 5.00e-02 4.00e+02 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 5 2.12 - 2.81: 5615 2.81 - 3.51: 25045 3.51 - 4.20: 35931 4.20 - 4.90: 58182 Nonbonded interactions: 124778 Sorted by model distance: nonbonded pdb=" CD1 ILE F 499 " pdb=" CD2 LEU F 626 " model vdw 1.419 3.880 nonbonded pdb=" CG1 ILE F 499 " pdb=" CD2 LEU F 626 " model vdw 1.759 3.860 nonbonded pdb=" O LEU F 626 " pdb=" N THR F 628 " model vdw 2.021 3.120 nonbonded pdb=" OH TYR F 335 " pdb=" O GLU F 369 " model vdw 2.047 3.040 nonbonded pdb=" O GLY A 365 " pdb=" OG SER A 368 " model vdw 2.115 3.040 ... (remaining 124773 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 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: 2.020 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 38.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 0.009 0.072 16661 Z= 0.569 Angle : 1.313 15.528 22796 Z= 0.912 Chirality : 0.056 0.331 2857 Planarity : 0.005 0.062 2999 Dihedral : 11.091 126.832 5270 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 7.04 % Allowed : 8.13 % Favored : 84.83 % Rotamer: Outliers : 0.37 % Allowed : 0.83 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % 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: -3.43 (0.16), residues: 2103 helix: -2.39 (0.10), residues: 1137 sheet: -3.80 (0.34), residues: 161 loop : -1.39 (0.25), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 300 HIS 0.009 0.002 HIS F 169 PHE 0.026 0.003 PHE A1376 TYR 0.028 0.003 TYR F 609 ARG 0.013 0.001 ARG F 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 330 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9296 (mttt) cc_final: 0.8835 (tttt) REVERT: A 193 MET cc_start: 0.8364 (mtm) cc_final: 0.8051 (mtm) REVERT: A 945 ILE cc_start: 0.9383 (mt) cc_final: 0.9135 (mm) REVERT: A 998 ASP cc_start: 0.8657 (m-30) cc_final: 0.8394 (m-30) REVERT: A 1005 MET cc_start: 0.9201 (tpt) cc_final: 0.8946 (mmt) REVERT: B 115 ILE cc_start: 0.2878 (mm) cc_final: 0.2669 (tp) REVERT: B 226 MET cc_start: -0.0924 (mmm) cc_final: -0.1302 (mmm) REVERT: B 394 ASP cc_start: 0.1764 (m-30) cc_final: 0.1475 (t0) REVERT: F 490 MET cc_start: 0.9114 (ttt) cc_final: 0.8637 (tmm) outliers start: 4 outliers final: 2 residues processed: 334 average time/residue: 0.2677 time to fit residues: 134.6606 Evaluate side-chains 225 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 111 optimal weight: 30.0000 chunk 88 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 66 optimal weight: 30.0000 chunk 104 optimal weight: 0.9980 chunk 127 optimal weight: 30.0000 chunk 198 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A 654 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 130 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 324 ASN B 363 HIS ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 ASN F 424 ASN F 447 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16661 Z= 0.242 Angle : 0.770 10.603 22796 Z= 0.405 Chirality : 0.042 0.264 2857 Planarity : 0.004 0.043 2999 Dihedral : 8.641 81.580 2942 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 2.90 % Allowed : 9.56 % Favored : 87.54 % Rotamer: Outliers : 0.28 % Allowed : 3.30 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.96 (0.18), residues: 2103 helix: -0.32 (0.13), residues: 1185 sheet: -3.64 (0.32), residues: 171 loop : -2.19 (0.25), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 403 HIS 0.011 0.002 HIS B 255 PHE 0.039 0.002 PHE A1376 TYR 0.025 0.002 TYR B 239 ARG 0.008 0.001 ARG F 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 288 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9303 (mttt) cc_final: 0.8696 (tmtt) REVERT: A 294 TRP cc_start: 0.8408 (p-90) cc_final: 0.8173 (p-90) REVERT: A 972 TYR cc_start: 0.7811 (t80) cc_final: 0.7593 (t80) REVERT: A 1128 ILE cc_start: 0.9555 (mt) cc_final: 0.9310 (tt) REVERT: A 1129 MET cc_start: 0.9435 (mmp) cc_final: 0.9173 (mmm) REVERT: A 1198 ILE cc_start: 0.9598 (mt) cc_final: 0.9309 (tp) REVERT: A 1328 ILE cc_start: 0.9252 (mt) cc_final: 0.8997 (tp) REVERT: A 1372 ILE cc_start: 0.9591 (mt) cc_final: 0.9277 (tp) REVERT: B 83 MET cc_start: 0.2508 (mmm) cc_final: 0.2168 (mmm) REVERT: B 368 MET cc_start: -0.1303 (ppp) cc_final: -0.1513 (ttt) REVERT: F 257 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8831 (tt) REVERT: F 424 ASN cc_start: 0.8745 (t0) cc_final: 0.7086 (t0) REVERT: F 490 MET cc_start: 0.9145 (ttt) cc_final: 0.8722 (tmm) outliers start: 3 outliers final: 1 residues processed: 291 average time/residue: 0.2488 time to fit residues: 112.1633 Evaluate side-chains 216 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 67 optimal weight: 20.0000 chunk 159 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 654 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 394 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 16661 Z= 0.227 Angle : 0.686 9.244 22796 Z= 0.361 Chirality : 0.040 0.252 2857 Planarity : 0.004 0.041 2999 Dihedral : 6.617 52.916 2942 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 2.52 % Allowed : 10.84 % Favored : 86.64 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % 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: -1.32 (0.18), residues: 2103 helix: 0.48 (0.14), residues: 1180 sheet: -3.52 (0.32), residues: 170 loop : -2.41 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1016 HIS 0.012 0.002 HIS F 308 PHE 0.039 0.002 PHE A 131 TYR 0.022 0.002 TYR F 413 ARG 0.006 0.001 ARG A1022 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9268 (mttt) cc_final: 0.8649 (tmtt) REVERT: A 282 MET cc_start: 0.8852 (tpt) cc_final: 0.8403 (tpp) REVERT: A 294 TRP cc_start: 0.8500 (p-90) cc_final: 0.8100 (p-90) REVERT: A 324 PHE cc_start: 0.9127 (m-80) cc_final: 0.8886 (m-80) REVERT: A 972 TYR cc_start: 0.8090 (t80) cc_final: 0.7704 (t80) REVERT: A 1129 MET cc_start: 0.9436 (mmp) cc_final: 0.9052 (mmp) REVERT: A 1198 ILE cc_start: 0.9603 (mt) cc_final: 0.9284 (tp) REVERT: A 1328 ILE cc_start: 0.9183 (mt) cc_final: 0.8887 (tp) REVERT: A 1372 ILE cc_start: 0.9649 (mt) cc_final: 0.9327 (tp) REVERT: B 83 MET cc_start: 0.2543 (mmm) cc_final: 0.2159 (mmm) REVERT: B 226 MET cc_start: -0.1233 (mmm) cc_final: -0.1492 (mmm) REVERT: B 368 MET cc_start: -0.1215 (ppp) cc_final: -0.1423 (ttt) REVERT: F 490 MET cc_start: 0.9174 (ttt) cc_final: 0.8715 (tmm) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2354 time to fit residues: 101.3533 Evaluate side-chains 220 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 0.0980 chunk 149 optimal weight: 0.0570 chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 104 optimal weight: 30.0000 chunk 189 optimal weight: 0.3980 chunk 57 optimal weight: 50.0000 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 ASN A 654 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16661 Z= 0.161 Angle : 0.642 11.078 22796 Z= 0.333 Chirality : 0.039 0.236 2857 Planarity : 0.003 0.035 2999 Dihedral : 6.079 53.616 2942 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 2.43 % Allowed : 9.32 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.87 (0.19), residues: 2103 helix: 0.92 (0.15), residues: 1193 sheet: -3.14 (0.34), residues: 162 loop : -2.48 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 122 HIS 0.011 0.001 HIS F 308 PHE 0.029 0.002 PHE A 131 TYR 0.017 0.002 TYR F 413 ARG 0.006 0.000 ARG F 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9317 (mttt) cc_final: 0.8651 (tmtt) REVERT: A 282 MET cc_start: 0.8752 (tpt) cc_final: 0.8467 (tpp) REVERT: A 290 THR cc_start: 0.9124 (p) cc_final: 0.8433 (p) REVERT: A 294 TRP cc_start: 0.8220 (p-90) cc_final: 0.7967 (p-90) REVERT: A 324 PHE cc_start: 0.9129 (m-80) cc_final: 0.8898 (m-80) REVERT: A 972 TYR cc_start: 0.7875 (t80) cc_final: 0.7507 (t80) REVERT: A 1051 LEU cc_start: 0.9234 (mm) cc_final: 0.8923 (mm) REVERT: A 1198 ILE cc_start: 0.9585 (mt) cc_final: 0.9255 (tp) REVERT: B 83 MET cc_start: 0.2565 (mmm) cc_final: 0.2185 (mmm) REVERT: B 226 MET cc_start: -0.1304 (mmm) cc_final: -0.1536 (mmm) REVERT: F 463 THR cc_start: 0.7245 (p) cc_final: 0.6955 (p) REVERT: F 490 MET cc_start: 0.9167 (ttt) cc_final: 0.8700 (tmm) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2334 time to fit residues: 102.1987 Evaluate side-chains 222 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 3.9990 chunk 120 optimal weight: 30.0000 chunk 3 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 108 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16661 Z= 0.248 Angle : 0.675 7.606 22796 Z= 0.356 Chirality : 0.041 0.239 2857 Planarity : 0.004 0.039 2999 Dihedral : 5.919 53.065 2942 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 2.38 % Allowed : 10.79 % Favored : 86.83 % Rotamer: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % 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 (0.19), residues: 2103 helix: 1.12 (0.15), residues: 1193 sheet: -3.12 (0.34), residues: 175 loop : -2.67 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 616 HIS 0.014 0.002 HIS B 255 PHE 0.043 0.002 PHE A 131 TYR 0.020 0.002 TYR A 313 ARG 0.007 0.001 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9295 (mttt) cc_final: 0.8650 (tmtt) REVERT: A 294 TRP cc_start: 0.8643 (p-90) cc_final: 0.8218 (p-90) REVERT: A 324 PHE cc_start: 0.9191 (m-80) cc_final: 0.8962 (m-80) REVERT: A 972 TYR cc_start: 0.8405 (t80) cc_final: 0.8045 (t80) REVERT: A 1051 LEU cc_start: 0.9280 (mm) cc_final: 0.8957 (mm) REVERT: A 1128 ILE cc_start: 0.9579 (mt) cc_final: 0.9275 (tt) REVERT: A 1198 ILE cc_start: 0.9606 (mt) cc_final: 0.9276 (tp) REVERT: A 1372 ILE cc_start: 0.9381 (tp) cc_final: 0.8949 (tp) REVERT: B 83 MET cc_start: 0.2547 (mmm) cc_final: 0.2144 (mmm) REVERT: B 226 MET cc_start: -0.0936 (mmm) cc_final: -0.1261 (mmm) REVERT: F 299 ASN cc_start: 0.8673 (t0) cc_final: 0.8453 (t0) REVERT: F 490 MET cc_start: 0.9205 (ttt) cc_final: 0.8731 (tmm) REVERT: F 493 ASP cc_start: 0.9107 (m-30) cc_final: 0.8720 (p0) REVERT: F 571 ASP cc_start: 0.8698 (m-30) cc_final: 0.8497 (m-30) REVERT: F 1011 LEU cc_start: 0.8937 (mt) cc_final: 0.8674 (mt) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.2301 time to fit residues: 92.4902 Evaluate side-chains 206 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 124 optimal weight: 30.0000 chunk 52 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 30.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 ASN A 654 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16661 Z= 0.201 Angle : 0.650 9.088 22796 Z= 0.339 Chirality : 0.040 0.235 2857 Planarity : 0.004 0.063 2999 Dihedral : 5.725 53.161 2942 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 2.28 % Allowed : 10.56 % Favored : 87.16 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % 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 (0.19), residues: 2103 helix: 1.24 (0.15), residues: 1200 sheet: -3.21 (0.34), residues: 162 loop : -2.64 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 245 HIS 0.013 0.002 HIS F 308 PHE 0.042 0.002 PHE A1376 TYR 0.030 0.002 TYR A 621 ARG 0.006 0.001 ARG F 398 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9278 (mttt) cc_final: 0.8624 (tmtt) REVERT: A 294 TRP cc_start: 0.8477 (p-90) cc_final: 0.8123 (p-90) REVERT: A 324 PHE cc_start: 0.9223 (m-80) cc_final: 0.8947 (m-80) REVERT: A 620 MET cc_start: 0.7988 (tmm) cc_final: 0.7768 (tmm) REVERT: A 972 TYR cc_start: 0.8356 (t80) cc_final: 0.8003 (t80) REVERT: A 1007 LEU cc_start: 0.9363 (tp) cc_final: 0.9052 (tp) REVERT: A 1051 LEU cc_start: 0.9239 (mm) cc_final: 0.8916 (mm) REVERT: A 1198 ILE cc_start: 0.9611 (mt) cc_final: 0.9259 (tp) REVERT: A 1372 ILE cc_start: 0.9438 (tp) cc_final: 0.9147 (tp) REVERT: B 83 MET cc_start: 0.2551 (mmm) cc_final: 0.2130 (mmm) REVERT: F 490 MET cc_start: 0.9223 (ttt) cc_final: 0.8754 (tmm) REVERT: F 493 ASP cc_start: 0.9111 (m-30) cc_final: 0.8735 (p0) REVERT: F 571 ASP cc_start: 0.8616 (m-30) cc_final: 0.8391 (m-30) REVERT: F 1012 MET cc_start: 0.8387 (mmp) cc_final: 0.8120 (mmp) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2306 time to fit residues: 95.0035 Evaluate side-chains 208 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 0.0040 chunk 23 optimal weight: 2.9990 chunk 120 optimal weight: 30.0000 chunk 154 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 178 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 211 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 ASN A 654 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16661 Z= 0.254 Angle : 0.674 8.226 22796 Z= 0.352 Chirality : 0.041 0.239 2857 Planarity : 0.004 0.037 2999 Dihedral : 5.693 55.605 2942 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 2.19 % Allowed : 11.55 % Favored : 86.26 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % 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 (0.19), residues: 2103 helix: 1.28 (0.15), residues: 1201 sheet: -3.14 (0.34), residues: 171 loop : -2.72 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 245 HIS 0.013 0.002 HIS F 308 PHE 0.036 0.002 PHE A1376 TYR 0.021 0.002 TYR A 313 ARG 0.006 0.001 ARG F 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9228 (mttt) cc_final: 0.8589 (tmtt) REVERT: A 294 TRP cc_start: 0.8631 (p-90) cc_final: 0.8182 (p-90) REVERT: A 324 PHE cc_start: 0.9228 (m-80) cc_final: 0.8974 (m-80) REVERT: A 1051 LEU cc_start: 0.9263 (mm) cc_final: 0.9026 (mm) REVERT: A 1198 ILE cc_start: 0.9614 (mt) cc_final: 0.9279 (tp) REVERT: A 1372 ILE cc_start: 0.9492 (tp) cc_final: 0.9139 (tp) REVERT: B 83 MET cc_start: 0.2688 (mmm) cc_final: 0.2260 (mmm) REVERT: F 289 ASP cc_start: 0.8243 (m-30) cc_final: 0.7897 (m-30) REVERT: F 490 MET cc_start: 0.9225 (ttt) cc_final: 0.8740 (tmm) REVERT: F 493 ASP cc_start: 0.9132 (m-30) cc_final: 0.8754 (p0) REVERT: F 571 ASP cc_start: 0.8630 (m-30) cc_final: 0.8384 (m-30) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2357 time to fit residues: 94.6113 Evaluate side-chains 208 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1374 ASN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16661 Z= 0.312 Angle : 0.724 8.504 22796 Z= 0.380 Chirality : 0.042 0.249 2857 Planarity : 0.004 0.051 2999 Dihedral : 5.887 53.424 2942 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 2.09 % Allowed : 11.51 % Favored : 86.40 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.68 (0.19), residues: 2103 helix: 1.25 (0.15), residues: 1206 sheet: -3.11 (0.35), residues: 168 loop : -2.81 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 245 HIS 0.012 0.002 HIS F 308 PHE 0.028 0.002 PHE A 127 TYR 0.028 0.002 TYR F 428 ARG 0.007 0.001 ARG F 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9212 (mttt) cc_final: 0.8557 (tmtt) REVERT: A 294 TRP cc_start: 0.8607 (p-90) cc_final: 0.8173 (p-90) REVERT: A 324 PHE cc_start: 0.9191 (m-80) cc_final: 0.8944 (m-80) REVERT: A 972 TYR cc_start: 0.6826 (t80) cc_final: 0.6535 (t80) REVERT: A 1168 LYS cc_start: 0.9281 (tptp) cc_final: 0.9027 (tmtt) REVERT: A 1198 ILE cc_start: 0.9624 (mt) cc_final: 0.9317 (tp) REVERT: A 1372 ILE cc_start: 0.9363 (tp) cc_final: 0.9015 (tp) REVERT: A 1376 PHE cc_start: 0.9490 (m-10) cc_final: 0.9264 (m-80) REVERT: B 83 MET cc_start: 0.2695 (mmm) cc_final: 0.2257 (mmm) REVERT: F 289 ASP cc_start: 0.8249 (m-30) cc_final: 0.7579 (m-30) REVERT: F 490 MET cc_start: 0.9226 (ttt) cc_final: 0.8723 (tmm) REVERT: F 571 ASP cc_start: 0.8697 (m-30) cc_final: 0.8434 (m-30) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2212 time to fit residues: 86.4674 Evaluate side-chains 208 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 60 optimal weight: 50.0000 chunk 177 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 ASN A 663 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16661 Z= 0.225 Angle : 0.677 9.145 22796 Z= 0.353 Chirality : 0.041 0.254 2857 Planarity : 0.004 0.059 2999 Dihedral : 5.644 53.193 2942 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 1.90 % Allowed : 11.46 % Favored : 86.64 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % 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: -0.60 (0.19), residues: 2103 helix: 1.33 (0.15), residues: 1211 sheet: -3.22 (0.35), residues: 158 loop : -2.80 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 245 HIS 0.011 0.002 HIS F 308 PHE 0.033 0.002 PHE A 127 TYR 0.037 0.002 TYR A1048 ARG 0.005 0.001 ARG F 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9215 (mttt) cc_final: 0.8527 (tmtt) REVERT: A 294 TRP cc_start: 0.8486 (p-90) cc_final: 0.8154 (p-90) REVERT: A 324 PHE cc_start: 0.9160 (m-80) cc_final: 0.8927 (m-80) REVERT: A 972 TYR cc_start: 0.6596 (t80) cc_final: 0.6241 (t80) REVERT: A 1168 LYS cc_start: 0.9211 (tptp) cc_final: 0.8964 (tmtt) REVERT: A 1198 ILE cc_start: 0.9611 (mt) cc_final: 0.9306 (tp) REVERT: A 1372 ILE cc_start: 0.9318 (tp) cc_final: 0.8917 (tp) REVERT: B 83 MET cc_start: 0.2678 (mmm) cc_final: 0.2237 (mmm) REVERT: F 289 ASP cc_start: 0.7922 (m-30) cc_final: 0.7312 (m-30) REVERT: F 490 MET cc_start: 0.9168 (ttt) cc_final: 0.8810 (tmm) REVERT: F 571 ASP cc_start: 0.8660 (m-30) cc_final: 0.8352 (m-30) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2255 time to fit residues: 91.5114 Evaluate side-chains 211 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 18 optimal weight: 0.0030 chunk 134 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN B 130 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16661 Z= 0.189 Angle : 0.650 9.400 22796 Z= 0.339 Chirality : 0.040 0.248 2857 Planarity : 0.004 0.057 2999 Dihedral : 5.432 53.202 2942 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 1.90 % Allowed : 10.70 % Favored : 87.40 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % 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: -0.44 (0.19), residues: 2103 helix: 1.44 (0.15), residues: 1211 sheet: -3.04 (0.35), residues: 159 loop : -2.73 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 245 HIS 0.011 0.002 HIS F 308 PHE 0.031 0.002 PHE A 127 TYR 0.024 0.002 TYR F 428 ARG 0.005 0.001 ARG F 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9202 (mttt) cc_final: 0.8508 (tmtt) REVERT: A 324 PHE cc_start: 0.9135 (m-80) cc_final: 0.8906 (m-80) REVERT: A 972 TYR cc_start: 0.6471 (t80) cc_final: 0.6166 (t80) REVERT: A 1168 LYS cc_start: 0.9176 (tptp) cc_final: 0.8700 (tmtt) REVERT: A 1198 ILE cc_start: 0.9609 (mt) cc_final: 0.9309 (tp) REVERT: A 1372 ILE cc_start: 0.9499 (tp) cc_final: 0.9267 (tp) REVERT: B 83 MET cc_start: 0.2693 (mmm) cc_final: 0.2242 (mmm) REVERT: F 235 ILE cc_start: 0.7767 (mt) cc_final: 0.7511 (mp) REVERT: F 289 ASP cc_start: 0.7984 (m-30) cc_final: 0.7394 (m-30) REVERT: F 490 MET cc_start: 0.9156 (ttt) cc_final: 0.8895 (tmm) REVERT: F 571 ASP cc_start: 0.8638 (m-30) cc_final: 0.8325 (m-30) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2172 time to fit residues: 89.8147 Evaluate side-chains 214 residues out of total 1895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 0.0770 chunk 53 optimal weight: 0.3980 chunk 160 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 50.0000 chunk 152 optimal weight: 30.0000 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.130869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.093905 restraints weight = 61410.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.091227 restraints weight = 48359.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.092106 restraints weight = 44370.929| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16661 Z= 0.156 Angle : 0.631 9.501 22796 Z= 0.327 Chirality : 0.039 0.246 2857 Planarity : 0.003 0.055 2999 Dihedral : 5.178 53.083 2942 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 1.76 % Allowed : 9.99 % Favored : 88.25 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % 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: -0.34 (0.19), residues: 2103 helix: 1.49 (0.15), residues: 1216 sheet: -2.86 (0.38), residues: 150 loop : -2.70 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 245 HIS 0.012 0.001 HIS F 308 PHE 0.029 0.002 PHE A 127 TYR 0.034 0.002 TYR A1048 ARG 0.007 0.000 ARG F 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3011.36 seconds wall clock time: 54 minutes 16.88 seconds (3256.88 seconds total)