Starting phenix.real_space_refine on Sat Sep 12 15:53:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jbr_6475/09_2026/3jbr_6475.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jbr_6475/09_2026/3jbr_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/3jbr_6475/09_2026/3jbr_6475.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jbr_6475/09_2026/3jbr_6475.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jbr_6475/09_2026/3jbr_6475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jbr_6475/09_2026/3jbr_6475.map" model { file = "/net/cci-nas-00/data/ceres_data/3jbr_6475/09_2026/3jbr_6475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jbr_6475/09_2026/3jbr_6475.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'PHE:plan': 39, 'GLN:plan1': 15, 'ASN:plan1': 29, 'ARG:plan': 32, 'GLU:plan': 34, 'TRP:plan': 10, 'TYR:plan': 27, 'ASP:plan': 21, 'HIS:plan': 12} 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: {'ARG:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLU:plan': 4, 'ARG:plan': 7, 'PHE:plan': 12, 'ASP:plan': 2, 'HIS:plan': 1, 'TRP:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 6} 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: {'UNK:plan-1': 16, 'HIS:plan': 3, 'GLN:plan1': 8, 'ASP:plan': 9, 'TYR:plan': 14, 'GLU:plan': 11, 'ASN:plan1': 7, 'TRP:plan': 1, 'ARG:plan': 3, 'PHE:plan': 2} 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: {'UNK:plan-1': 226, 'GLU:plan': 2, 'GLN:plan1': 5, 'TYR:plan': 2, 'PHE:plan': 3, 'ASP:plan': 8, '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 chiralities: 17 Time building chain proxies: 2.99, per 1000 atoms: 0.18 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: 1.16 Conformation dependent library (CDL) restraints added in 569.6 milliseconds 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: 0.30 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: 2.72 Time building geometry restraints manager: 1.49 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 - 16.35: 9489 16.35 - 32.69: 147 32.69 - 49.04: 41 49.04 - 65.38: 5 65.38 - 81.73: 5 Dihedral angle restraints: 9687 sinusoidal: 2399 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 9684 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: 0.970 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.610 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 16663 Z= 0.562 Angle : 1.341 29.419 22801 Z= 0.921 Chirality : 0.056 0.331 2857 Planarity : 0.005 0.062 2999 Dihedral : 8.319 81.729 4917 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 19.26 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.013 0.001 ARG F 218 TYR 0.028 0.003 TYR F 609 PHE 0.026 0.003 PHE A1376 TRP 0.032 0.003 TRP A 300 HIS 0.009 0.002 HIS F 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00860 / 0.56 (16661) covalent geometry : angle 1.31276 / 0.91 (22796) SS BOND : bond 0.00194 / 0.10 ( 1) SS BOND : angle 29.05706 / 16.24 ( 2) hydrogen bonds : bond 0.17855 / 11.79 ( 1036) hydrogen bonds : angle 9.59197 / 6.90 ( 3000) link_TRANS : bond 0.01382 / 0.73 ( 1) link_TRANS : angle 1.83381 / 0.69 ( 3) *********************** 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 to be fit. rotamer outliers: 4 poor density : 330 time to evaluate : 0.527 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: 0.8837 (tttt) REVERT: A 193 MET cc_start: 0.8364 (mtm) cc_final: 0.8050 (mtm) REVERT: A 938 LEU cc_start: 0.9336 (mt) cc_final: 0.9134 (mt) REVERT: A 945 ILE cc_start: 0.9383 (mt) cc_final: 0.9122 (mm) REVERT: A 998 ASP cc_start: 0.8657 (m-30) cc_final: 0.8397 (m-30) REVERT: A 1005 MET cc_start: 0.9201 (tpt) cc_final: 0.8963 (mmt) REVERT: B 226 MET cc_start: -0.0924 (mmm) cc_final: -0.1314 (mmm) REVERT: B 394 ASP cc_start: 0.1764 (m-30) cc_final: 0.1469 (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: 0.1120 time to fit residues: 57.6272 Evaluate side-chains 226 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A 654 ASN ** A1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 311 GLN F 316 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 ASN F 424 ASN F 447 GLN ** F 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.129778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.091631 restraints weight = 63597.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.089515 restraints weight = 47315.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.090199 restraints weight = 39680.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.090769 restraints weight = 29525.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.090971 restraints weight = 25160.878| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16663 Z= 0.182 Angle : 0.758 10.668 22801 Z= 0.402 Chirality : 0.041 0.266 2857 Planarity : 0.004 0.044 2999 Dihedral : 6.012 34.631 2589 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 3.00 % Allowed : 9.94 % Favored : 87.07 % Rotamer: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.18), residues: 2103 helix: -0.39 (0.13), residues: 1185 sheet: -3.65 (0.32), residues: 171 loop : -2.15 (0.25), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1242 TYR 0.024 0.002 TYR B 239 PHE 0.038 0.002 PHE A 131 TRP 0.013 0.002 TRP F 403 HIS 0.010 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (16661) covalent geometry : angle 0.75742 / 0.40 (22796) SS BOND : bond 0.01105 / 0.58 ( 1) SS BOND : angle 2.02232 / 1.06 ( 2) hydrogen bonds : bond 0.04781 / 3.24 ( 1036) hydrogen bonds : angle 5.98855 / 4.36 ( 3000) link_TRANS : bond 0.00054 / 0.03 ( 1) link_TRANS : angle 0.30517 / 0.15 ( 3) *********************** 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 290 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 288 time to evaluate : 0.505 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: symmetry clash REVERT: A 88 LYS cc_start: 0.9068 (mttt) cc_final: 0.8406 (tmtt) REVERT: A 131 PHE cc_start: 0.8666 (t80) cc_final: 0.8437 (t80) REVERT: A 294 TRP cc_start: 0.9001 (p-90) cc_final: 0.8607 (p-90) REVERT: A 327 ASN cc_start: 0.8768 (m110) cc_final: 0.8510 (m110) REVERT: A 614 GLU cc_start: 0.8264 (tm-30) cc_final: 0.8061 (tm-30) REVERT: A 1128 ILE cc_start: 0.9613 (mt) cc_final: 0.9013 (tt) REVERT: A 1129 MET cc_start: 0.8965 (mmp) cc_final: 0.8300 (mmp) REVERT: A 1372 ILE cc_start: 0.9686 (mt) cc_final: 0.9242 (tp) REVERT: F 242 ARG cc_start: 0.8418 (tpp80) cc_final: 0.8121 (mmt-90) REVERT: F 257 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8485 (tt) REVERT: F 424 ASN cc_start: 0.8952 (t0) cc_final: 0.6993 (t0) REVERT: F 483 ASN cc_start: 0.8904 (m-40) cc_final: 0.8583 (m-40) REVERT: F 490 MET cc_start: 0.8325 (ttt) cc_final: 0.8067 (tmm) REVERT: F 571 ASP cc_start: 0.8759 (m-30) cc_final: 0.8494 (m-30) outliers start: 2 outliers final: 1 residues processed: 290 average time/residue: 0.1110 time to fit residues: 50.5776 Evaluate side-chains 221 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 134 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 184 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 chunk 42 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 617 ASN A 654 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN B 246 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.130269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.091252 restraints weight = 62967.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.088481 restraints weight = 53968.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.089137 restraints weight = 42604.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.089947 restraints weight = 32790.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.089919 restraints weight = 28117.182| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16663 Z= 0.159 Angle : 0.691 9.149 22801 Z= 0.365 Chirality : 0.040 0.258 2857 Planarity : 0.004 0.041 2999 Dihedral : 5.492 30.176 2589 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 2.66 % Allowed : 10.79 % Favored : 86.54 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.18), residues: 2103 helix: 0.47 (0.14), residues: 1180 sheet: -3.51 (0.32), residues: 170 loop : -2.38 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1022 TYR 0.022 0.002 TYR A 972 PHE 0.043 0.002 PHE A 131 TRP 0.020 0.002 TRP F 403 HIS 0.009 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (16661) covalent geometry : angle 0.69085 / 0.36 (22796) SS BOND : bond 0.01460 / 0.77 ( 1) SS BOND : angle 0.49894 / 0.28 ( 2) hydrogen bonds : bond 0.04091 / 2.77 ( 1036) hydrogen bonds : angle 5.31753 / 3.88 ( 3000) link_TRANS : bond 0.00124 / 0.07 ( 1) link_TRANS : angle 0.33607 / 0.17 ( 3) *********************** 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 267 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.441 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: 0.9074 (mttt) cc_final: 0.8353 (tmtt) REVERT: A 123 ASN cc_start: 0.9721 (m110) cc_final: 0.9485 (m110) REVERT: A 282 MET cc_start: 0.8736 (tpt) cc_final: 0.8060 (tpp) REVERT: A 294 TRP cc_start: 0.9046 (p-90) cc_final: 0.8588 (p-90) REVERT: A 296 ASP cc_start: 0.8899 (m-30) cc_final: 0.8674 (m-30) REVERT: A 320 LEU cc_start: 0.9545 (mt) cc_final: 0.9294 (mt) REVERT: A 324 PHE cc_start: 0.9136 (m-80) cc_final: 0.8674 (m-80) REVERT: A 1007 LEU cc_start: 0.8955 (tp) cc_final: 0.8705 (tp) REVERT: A 1129 MET cc_start: 0.8954 (mmp) cc_final: 0.8463 (mmp) REVERT: A 1372 ILE cc_start: 0.9738 (mt) cc_final: 0.9315 (tp) REVERT: A 1376 PHE cc_start: 0.9015 (m-80) cc_final: 0.8677 (m-80) REVERT: B 226 MET cc_start: -0.1657 (mmm) cc_final: -0.1963 (mmm) REVERT: F 424 ASN cc_start: 0.8465 (t0) cc_final: 0.7976 (t0) REVERT: F 490 MET cc_start: 0.8535 (ttt) cc_final: 0.8141 (tmm) REVERT: F 505 ARG cc_start: 0.7594 (ttt-90) cc_final: 0.7276 (ttt180) REVERT: F 571 ASP cc_start: 0.8690 (m-30) cc_final: 0.8337 (m-30) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1016 time to fit residues: 43.6078 Evaluate side-chains 221 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 13 optimal weight: 7.9990 chunk 188 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 207 optimal weight: 0.9990 chunk 63 optimal weight: 40.0000 chunk 84 optimal weight: 8.9990 chunk 102 optimal weight: 0.4980 chunk 150 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 654 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.129262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.091980 restraints weight = 63367.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.088693 restraints weight = 52315.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.089790 restraints weight = 43394.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.089905 restraints weight = 32377.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.090745 restraints weight = 30071.308| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16663 Z= 0.167 Angle : 0.671 9.982 22801 Z= 0.352 Chirality : 0.040 0.221 2857 Planarity : 0.004 0.037 2999 Dihedral : 5.325 29.057 2589 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 2.47 % Allowed : 10.41 % Favored : 87.11 % Rotamer: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 2103 helix: 0.84 (0.15), residues: 1193 sheet: -3.41 (0.34), residues: 165 loop : -2.59 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 353 TYR 0.024 0.002 TYR F 413 PHE 0.029 0.002 PHE A1376 TRP 0.024 0.002 TRP A1016 HIS 0.011 0.002 HIS F 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (16661) covalent geometry : angle 0.67129 / 0.35 (22796) SS BOND : bond 0.00062 / 0.03 ( 1) SS BOND : angle 0.40808 / 0.22 ( 2) hydrogen bonds : bond 0.03780 / 2.57 ( 1036) hydrogen bonds : angle 4.99219 / 3.64 ( 3000) link_TRANS : bond 0.00121 / 0.06 ( 1) link_TRANS : angle 0.32391 / 0.16 ( 3) *********************** 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 258 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9092 (mttt) cc_final: 0.8317 (tmtt) REVERT: A 193 MET cc_start: 0.8419 (mtm) cc_final: 0.8216 (mtm) REVERT: A 282 MET cc_start: 0.8695 (tpt) cc_final: 0.8093 (tpp) REVERT: A 294 TRP cc_start: 0.9065 (p-90) cc_final: 0.8550 (p-90) REVERT: A 296 ASP cc_start: 0.8890 (m-30) cc_final: 0.8644 (m-30) REVERT: A 320 LEU cc_start: 0.9431 (mt) cc_final: 0.9199 (mt) REVERT: A 324 PHE cc_start: 0.9080 (m-80) cc_final: 0.8628 (m-80) REVERT: A 1004 MET cc_start: 0.6949 (tmm) cc_final: 0.6656 (tmm) REVERT: A 1129 MET cc_start: 0.9069 (mmp) cc_final: 0.8848 (mmm) REVERT: A 1130 LEU cc_start: 0.9181 (mt) cc_final: 0.8977 (mt) REVERT: A 1326 GLN cc_start: 0.8668 (pp30) cc_final: 0.8459 (pp30) REVERT: A 1372 ILE cc_start: 0.9731 (mt) cc_final: 0.9237 (tp) REVERT: A 1376 PHE cc_start: 0.8987 (m-80) cc_final: 0.8692 (m-80) REVERT: B 226 MET cc_start: -0.1352 (mmm) cc_final: -0.1713 (mmm) REVERT: F 299 ASN cc_start: 0.8634 (t0) cc_final: 0.8342 (t0) REVERT: F 490 MET cc_start: 0.8455 (ttt) cc_final: 0.8137 (tmm) REVERT: F 505 ARG cc_start: 0.7533 (ttt-90) cc_final: 0.7301 (ttt180) REVERT: F 571 ASP cc_start: 0.8626 (m-30) cc_final: 0.8170 (m-30) REVERT: F 1012 MET cc_start: 0.7889 (mmp) cc_final: 0.7675 (mmp) outliers start: 1 outliers final: 1 residues processed: 258 average time/residue: 0.0985 time to fit residues: 41.7300 Evaluate side-chains 218 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 24 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 128 optimal weight: 40.0000 chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 186 optimal weight: 0.3980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 654 ASN A 958 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.130345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.091549 restraints weight = 63363.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.091222 restraints weight = 55379.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091637 restraints weight = 38646.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.092205 restraints weight = 30173.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.092434 restraints weight = 26367.569| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16663 Z= 0.139 Angle : 0.643 8.040 22801 Z= 0.337 Chirality : 0.040 0.229 2857 Planarity : 0.003 0.047 2999 Dihedral : 5.037 28.983 2589 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 2.38 % Allowed : 10.51 % Favored : 87.11 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 2103 helix: 1.19 (0.15), residues: 1201 sheet: -3.15 (0.36), residues: 161 loop : -2.62 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 353 TYR 0.015 0.001 TYR F 413 PHE 0.031 0.002 PHE A 131 TRP 0.014 0.001 TRP A1016 HIS 0.012 0.002 HIS F 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (16661) covalent geometry : angle 0.64344 / 0.34 (22796) SS BOND : bond 0.01825 / 0.96 ( 1) SS BOND : angle 0.78065 / 0.45 ( 2) hydrogen bonds : bond 0.03538 / 2.41 ( 1036) hydrogen bonds : angle 4.70990 / 3.43 ( 3000) link_TRANS : bond 0.00111 / 0.06 ( 1) link_TRANS : angle 0.26600 / 0.13 ( 3) *********************** 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 267 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9106 (mttt) cc_final: 0.8275 (tmtt) REVERT: A 282 MET cc_start: 0.8686 (tpt) cc_final: 0.8031 (tpp) REVERT: A 294 TRP cc_start: 0.8977 (p-90) cc_final: 0.8458 (p-90) REVERT: A 296 ASP cc_start: 0.8981 (m-30) cc_final: 0.8726 (m-30) REVERT: A 320 LEU cc_start: 0.9534 (mt) cc_final: 0.9282 (mt) REVERT: A 324 PHE cc_start: 0.9250 (m-80) cc_final: 0.8768 (m-80) REVERT: A 972 TYR cc_start: 0.6391 (t80) cc_final: 0.6159 (t80) REVERT: A 998 ASP cc_start: 0.8544 (m-30) cc_final: 0.8115 (m-30) REVERT: A 1129 MET cc_start: 0.9112 (mmp) cc_final: 0.8723 (mmp) REVERT: A 1326 GLN cc_start: 0.8625 (pp30) cc_final: 0.8420 (pp30) REVERT: A 1372 ILE cc_start: 0.9738 (mt) cc_final: 0.9243 (tp) REVERT: A 1376 PHE cc_start: 0.9004 (m-80) cc_final: 0.8761 (m-80) REVERT: B 226 MET cc_start: -0.1224 (mmm) cc_final: -0.1451 (mmm) REVERT: B 245 MET cc_start: 0.2383 (ppp) cc_final: 0.1162 (ptt) REVERT: F 281 MET cc_start: 0.8760 (tpt) cc_final: 0.8109 (tpt) REVERT: F 299 ASN cc_start: 0.8661 (t0) cc_final: 0.8433 (t0) REVERT: F 490 MET cc_start: 0.8497 (ttt) cc_final: 0.8130 (tmm) REVERT: F 493 ASP cc_start: 0.8528 (m-30) cc_final: 0.8317 (p0) REVERT: F 505 ARG cc_start: 0.7473 (ttt-90) cc_final: 0.7195 (ttt180) REVERT: F 571 ASP cc_start: 0.8590 (m-30) cc_final: 0.8134 (m-30) REVERT: F 1011 LEU cc_start: 0.8646 (mt) cc_final: 0.8261 (mt) REVERT: F 1012 MET cc_start: 0.7813 (mmp) cc_final: 0.7483 (mmp) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.0997 time to fit residues: 42.9527 Evaluate side-chains 223 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 81 optimal weight: 3.9990 chunk 149 optimal weight: 0.0010 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.0010 chunk 0 optimal weight: 30.0000 chunk 174 optimal weight: 0.2980 chunk 89 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 212 optimal weight: 0.0470 chunk 164 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 overall best weight: 0.8692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 HIS A 617 ASN 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 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.131754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.092898 restraints weight = 63140.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.090639 restraints weight = 50194.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.091191 restraints weight = 42990.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.091856 restraints weight = 31295.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.091954 restraints weight = 26353.019| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16663 Z= 0.121 Angle : 0.621 7.984 22801 Z= 0.323 Chirality : 0.039 0.232 2857 Planarity : 0.003 0.040 2999 Dihedral : 4.857 27.968 2589 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 2.23 % Allowed : 9.94 % Favored : 87.83 % Rotamer: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.19), residues: 2103 helix: 1.35 (0.15), residues: 1206 sheet: -2.91 (0.37), residues: 144 loop : -2.62 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 243 TYR 0.018 0.001 TYR F 238 PHE 0.028 0.001 PHE A1376 TRP 0.023 0.001 TRP A1016 HIS 0.012 0.002 HIS F 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (16661) covalent geometry : angle 0.62107 / 0.32 (22796) SS BOND : bond 0.00826 / 0.43 ( 1) SS BOND : angle 2.49849 / 1.36 ( 2) hydrogen bonds : bond 0.03268 / 2.23 ( 1036) hydrogen bonds : angle 4.53405 / 3.29 ( 3000) link_TRANS : bond 0.00104 / 0.05 ( 1) link_TRANS : angle 0.25198 / 0.13 ( 3) *********************** 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 270 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9070 (mttt) cc_final: 0.8258 (tmtt) REVERT: A 282 MET cc_start: 0.8556 (tpt) cc_final: 0.7867 (tpp) REVERT: A 294 TRP cc_start: 0.8840 (p-90) cc_final: 0.8513 (p-90) REVERT: A 296 ASP cc_start: 0.8925 (m-30) cc_final: 0.8660 (m-30) REVERT: A 320 LEU cc_start: 0.9388 (mt) cc_final: 0.9163 (mt) REVERT: A 324 PHE cc_start: 0.9147 (m-80) cc_final: 0.8666 (m-80) REVERT: A 620 MET cc_start: 0.7410 (ttm) cc_final: 0.7169 (ttm) REVERT: A 652 LEU cc_start: 0.9308 (tt) cc_final: 0.8984 (tt) REVERT: A 656 PHE cc_start: 0.9145 (m-80) cc_final: 0.8795 (m-80) REVERT: A 940 PHE cc_start: 0.8979 (m-80) cc_final: 0.8777 (m-80) REVERT: A 998 ASP cc_start: 0.8455 (m-30) cc_final: 0.8108 (m-30) REVERT: A 1004 MET cc_start: 0.6889 (tmm) cc_final: 0.6665 (tmm) REVERT: A 1007 LEU cc_start: 0.9070 (tp) cc_final: 0.8597 (tp) REVERT: A 1051 LEU cc_start: 0.9277 (mm) cc_final: 0.8803 (mm) REVERT: A 1125 PHE cc_start: 0.9039 (t80) cc_final: 0.8714 (t80) REVERT: A 1129 MET cc_start: 0.9124 (mmp) cc_final: 0.8715 (mmp) REVERT: A 1372 ILE cc_start: 0.9702 (mt) cc_final: 0.9164 (tp) REVERT: B 226 MET cc_start: -0.1133 (mmm) cc_final: -0.1417 (mmm) REVERT: B 245 MET cc_start: 0.2552 (ppp) cc_final: 0.1455 (ptt) REVERT: F 299 ASN cc_start: 0.8657 (t0) cc_final: 0.8353 (t0) REVERT: F 493 ASP cc_start: 0.8535 (m-30) cc_final: 0.8229 (p0) REVERT: F 505 ARG cc_start: 0.7292 (ttt-90) cc_final: 0.7001 (ttt180) REVERT: F 571 ASP cc_start: 0.8518 (m-30) cc_final: 0.8177 (m-30) REVERT: F 1011 LEU cc_start: 0.8549 (mt) cc_final: 0.8243 (mt) REVERT: F 1012 MET cc_start: 0.7673 (mmp) cc_final: 0.7393 (mmp) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.1039 time to fit residues: 44.4320 Evaluate side-chains 216 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 145 optimal weight: 0.0470 chunk 182 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 216 optimal weight: 0.3980 chunk 177 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 164 optimal weight: 20.0000 chunk 211 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 HIS A 617 ASN A 654 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.132029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.094020 restraints weight = 64627.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.091369 restraints weight = 48313.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.092103 restraints weight = 42497.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.092333 restraints weight = 28449.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.092548 restraints weight = 25478.809| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16663 Z= 0.120 Angle : 0.610 8.371 22801 Z= 0.318 Chirality : 0.039 0.238 2857 Planarity : 0.004 0.115 2999 Dihedral : 4.704 28.377 2589 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 2.09 % Allowed : 9.94 % Favored : 87.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 2103 helix: 1.43 (0.15), residues: 1209 sheet: -2.83 (0.38), residues: 146 loop : -2.59 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 242 TYR 0.018 0.001 TYR A 91 PHE 0.033 0.001 PHE A1376 TRP 0.032 0.001 TRP F 245 HIS 0.011 0.002 HIS F 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (16661) covalent geometry : angle 0.60931 / 0.32 (22796) SS BOND : bond 0.02244 / 1.18 ( 1) SS BOND : angle 2.48522 / 1.37 ( 2) hydrogen bonds : bond 0.03221 / 2.18 ( 1036) hydrogen bonds : angle 4.42880 / 3.21 ( 3000) link_TRANS : bond 0.00099 / 0.05 ( 1) link_TRANS : angle 0.26971 / 0.14 ( 3) *********************** 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 264 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9080 (mttt) cc_final: 0.8231 (tmtt) REVERT: A 296 ASP cc_start: 0.8932 (m-30) cc_final: 0.8677 (m-30) REVERT: A 320 LEU cc_start: 0.9513 (mt) cc_final: 0.9247 (mt) REVERT: A 324 PHE cc_start: 0.9214 (m-80) cc_final: 0.8744 (m-80) REVERT: A 620 MET cc_start: 0.7449 (ttm) cc_final: 0.7246 (ttm) REVERT: A 652 LEU cc_start: 0.9284 (tt) cc_final: 0.8856 (tp) REVERT: A 656 PHE cc_start: 0.9328 (m-80) cc_final: 0.8953 (m-80) REVERT: A 940 PHE cc_start: 0.9088 (m-80) cc_final: 0.8870 (m-80) REVERT: A 998 ASP cc_start: 0.8348 (m-30) cc_final: 0.7863 (p0) REVERT: A 1004 MET cc_start: 0.6893 (tmm) cc_final: 0.6618 (tmm) REVERT: A 1007 LEU cc_start: 0.9075 (tp) cc_final: 0.8775 (tp) REVERT: A 1014 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7609 (pp20) REVERT: A 1123 LEU cc_start: 0.9429 (tt) cc_final: 0.9144 (tp) REVERT: A 1125 PHE cc_start: 0.9022 (t80) cc_final: 0.8668 (t80) REVERT: A 1129 MET cc_start: 0.9099 (mmp) cc_final: 0.8699 (mmp) REVERT: A 1323 GLU cc_start: 0.8432 (tp30) cc_final: 0.8197 (tt0) REVERT: A 1365 TYR cc_start: 0.8250 (t80) cc_final: 0.7804 (t80) REVERT: A 1372 ILE cc_start: 0.9735 (mt) cc_final: 0.9300 (tp) REVERT: A 1376 PHE cc_start: 0.8897 (m-80) cc_final: 0.8670 (m-80) REVERT: B 226 MET cc_start: -0.1210 (mmm) cc_final: -0.1470 (mmm) REVERT: B 245 MET cc_start: 0.2452 (ppp) cc_final: 0.1411 (ptt) REVERT: F 235 ILE cc_start: 0.8127 (mt) cc_final: 0.7887 (mp) REVERT: F 289 ASP cc_start: 0.8624 (m-30) cc_final: 0.8019 (m-30) REVERT: F 299 ASN cc_start: 0.8681 (t0) cc_final: 0.8351 (t0) REVERT: F 493 ASP cc_start: 0.8542 (m-30) cc_final: 0.8244 (p0) REVERT: F 505 ARG cc_start: 0.7207 (ttt-90) cc_final: 0.7002 (ttt180) REVERT: F 571 ASP cc_start: 0.8607 (m-30) cc_final: 0.8268 (m-30) REVERT: F 1011 LEU cc_start: 0.8442 (mt) cc_final: 0.8176 (mt) REVERT: F 1012 MET cc_start: 0.7613 (mmp) cc_final: 0.7393 (mmp) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.0978 time to fit residues: 42.1530 Evaluate side-chains 220 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 63 optimal weight: 6.9990 chunk 78 optimal weight: 0.0870 chunk 7 optimal weight: 0.0570 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 136 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 159 optimal weight: 40.0000 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 617 ASN A 654 ASN ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN F 311 GLN F 408 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.131614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.094126 restraints weight = 61659.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.091475 restraints weight = 46747.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.092474 restraints weight = 37775.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.092880 restraints weight = 28853.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.092858 restraints weight = 26582.090| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16663 Z= 0.123 Angle : 0.619 9.846 22801 Z= 0.322 Chirality : 0.039 0.243 2857 Planarity : 0.004 0.076 2999 Dihedral : 4.649 28.782 2589 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 1.95 % Allowed : 9.70 % Favored : 88.35 % Rotamer: Outliers : 0.09 % Allowed : 1.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.19), residues: 2103 helix: 1.57 (0.15), residues: 1205 sheet: -2.71 (0.39), residues: 146 loop : -2.62 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 242 TYR 0.012 0.001 TYR F 413 PHE 0.027 0.001 PHE A1376 TRP 0.031 0.002 TRP F 245 HIS 0.013 0.002 HIS F 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (16661) covalent geometry : angle 0.61938 / 0.32 (22796) SS BOND : bond 0.00863 / 0.45 ( 1) SS BOND : angle 1.19941 / 0.66 ( 2) hydrogen bonds : bond 0.03130 / 2.12 ( 1036) hydrogen bonds : angle 4.37348 / 3.17 ( 3000) link_TRANS : bond 0.00093 / 0.05 ( 1) link_TRANS : angle 0.26371 / 0.13 ( 3) *********************** 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 265 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9067 (mttt) cc_final: 0.8218 (tmtt) REVERT: A 123 ASN cc_start: 0.9702 (m110) cc_final: 0.9470 (m110) REVERT: A 296 ASP cc_start: 0.8895 (m-30) cc_final: 0.8614 (m-30) REVERT: A 320 LEU cc_start: 0.9302 (mt) cc_final: 0.9101 (mt) REVERT: A 324 PHE cc_start: 0.9108 (m-80) cc_final: 0.8633 (m-80) REVERT: A 617 ASN cc_start: 0.6825 (t160) cc_final: 0.6579 (t0) REVERT: A 652 LEU cc_start: 0.9298 (tt) cc_final: 0.8812 (tp) REVERT: A 656 PHE cc_start: 0.9349 (m-80) cc_final: 0.8925 (m-80) REVERT: A 998 ASP cc_start: 0.8349 (m-30) cc_final: 0.7889 (p0) REVERT: A 1007 LEU cc_start: 0.9181 (tp) cc_final: 0.8754 (tp) REVERT: A 1125 PHE cc_start: 0.8957 (t80) cc_final: 0.8579 (t80) REVERT: A 1129 MET cc_start: 0.9089 (mmp) cc_final: 0.8652 (mmp) REVERT: A 1137 MET cc_start: 0.7817 (ptt) cc_final: 0.7447 (ppp) REVERT: A 1237 LEU cc_start: 0.9117 (tp) cc_final: 0.8567 (tp) REVERT: A 1365 TYR cc_start: 0.8079 (t80) cc_final: 0.7735 (t80) REVERT: A 1372 ILE cc_start: 0.9691 (mt) cc_final: 0.9251 (tp) REVERT: B 226 MET cc_start: -0.1128 (mmm) cc_final: -0.1417 (mmm) REVERT: B 245 MET cc_start: 0.2687 (ppp) cc_final: 0.1655 (ptt) REVERT: F 299 ASN cc_start: 0.8582 (t0) cc_final: 0.8254 (t0) REVERT: F 474 GLN cc_start: 0.6420 (tt0) cc_final: 0.6157 (mm-40) REVERT: F 493 ASP cc_start: 0.8433 (m-30) cc_final: 0.8195 (p0) REVERT: F 571 ASP cc_start: 0.8466 (m-30) cc_final: 0.8144 (m-30) outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.0974 time to fit residues: 42.3073 Evaluate side-chains 220 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 76 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 163 optimal weight: 0.3980 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 59 optimal weight: 50.0000 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 40.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 617 ASN A 654 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN F 408 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.131956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.095421 restraints weight = 62291.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.091849 restraints weight = 47846.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.092428 restraints weight = 46579.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.093114 restraints weight = 34609.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.093302 restraints weight = 30710.165| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16663 Z= 0.122 Angle : 0.614 8.859 22801 Z= 0.320 Chirality : 0.039 0.249 2857 Planarity : 0.003 0.049 2999 Dihedral : 4.555 27.586 2589 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 1.81 % Allowed : 10.18 % Favored : 88.02 % Rotamer: Outliers : 0.18 % Allowed : 0.46 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 2103 helix: 1.63 (0.15), residues: 1208 sheet: -2.59 (0.38), residues: 155 loop : -2.62 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 242 TYR 0.019 0.001 TYR F 413 PHE 0.033 0.001 PHE A 127 TRP 0.033 0.002 TRP A 294 HIS 0.019 0.002 HIS F 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (16661) covalent geometry : angle 0.61436 / 0.32 (22796) SS BOND : bond 0.01256 / 0.66 ( 1) SS BOND : angle 0.59495 / 0.32 ( 2) hydrogen bonds : bond 0.03056 / 2.07 ( 1036) hydrogen bonds : angle 4.30242 / 3.12 ( 3000) link_TRANS : bond 0.00089 / 0.05 ( 1) link_TRANS : angle 0.26626 / 0.13 ( 3) *********************** 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 263 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9057 (mttt) cc_final: 0.8209 (tmtt) REVERT: A 294 TRP cc_start: 0.8899 (p-90) cc_final: 0.8620 (p-90) REVERT: A 320 LEU cc_start: 0.9365 (mt) cc_final: 0.9156 (mt) REVERT: A 324 PHE cc_start: 0.9175 (m-80) cc_final: 0.8695 (m-80) REVERT: A 620 MET cc_start: 0.7139 (ttm) cc_final: 0.6858 (mtm) REVERT: A 652 LEU cc_start: 0.9326 (tt) cc_final: 0.8843 (tp) REVERT: A 656 PHE cc_start: 0.9353 (m-80) cc_final: 0.8924 (m-80) REVERT: A 998 ASP cc_start: 0.8375 (m-30) cc_final: 0.7902 (p0) REVERT: A 1007 LEU cc_start: 0.9055 (tp) cc_final: 0.8749 (tp) REVERT: A 1125 PHE cc_start: 0.9009 (t80) cc_final: 0.8635 (t80) REVERT: A 1129 MET cc_start: 0.9151 (mmp) cc_final: 0.8804 (mmp) REVERT: A 1137 MET cc_start: 0.7874 (ptt) cc_final: 0.7545 (ppp) REVERT: A 1189 ILE cc_start: 0.9601 (mt) cc_final: 0.8873 (mt) REVERT: A 1241 MET cc_start: 0.8708 (mmp) cc_final: 0.8441 (tmm) REVERT: A 1365 TYR cc_start: 0.8115 (t80) cc_final: 0.7861 (t80) REVERT: A 1372 ILE cc_start: 0.9717 (mt) cc_final: 0.9453 (mm) REVERT: B 226 MET cc_start: -0.1243 (mmm) cc_final: -0.1464 (mmm) REVERT: B 245 MET cc_start: 0.2617 (ppp) cc_final: 0.1703 (ptt) REVERT: F 271 LEU cc_start: 0.9130 (tt) cc_final: 0.8671 (mt) REVERT: F 299 ASN cc_start: 0.8776 (t0) cc_final: 0.8389 (t0) REVERT: F 474 GLN cc_start: 0.6457 (tt0) cc_final: 0.6143 (mm-40) REVERT: F 571 ASP cc_start: 0.8637 (m-30) cc_final: 0.8290 (m-30) outliers start: 2 outliers final: 0 residues processed: 262 average time/residue: 0.1010 time to fit residues: 42.8224 Evaluate side-chains 216 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 118 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 62 optimal weight: 30.0000 chunk 14 optimal weight: 1.9990 chunk 126 optimal weight: 40.0000 chunk 102 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 617 ASN A 654 ASN B 130 GLN ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.132180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.094861 restraints weight = 60534.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.092738 restraints weight = 46726.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.093221 restraints weight = 35802.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.093338 restraints weight = 31844.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.093605 restraints weight = 28644.902| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16663 Z= 0.117 Angle : 0.614 8.486 22801 Z= 0.319 Chirality : 0.039 0.253 2857 Planarity : 0.004 0.061 2999 Dihedral : 4.494 27.974 2589 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 1.76 % Allowed : 9.80 % Favored : 88.45 % Rotamer: Outliers : 0.09 % Allowed : 0.73 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 2103 helix: 1.75 (0.15), residues: 1203 sheet: -2.52 (0.39), residues: 155 loop : -2.60 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 422 TYR 0.023 0.001 TYR F 428 PHE 0.031 0.001 PHE A1376 TRP 0.035 0.002 TRP F 245 HIS 0.018 0.002 HIS F 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (16661) covalent geometry : angle 0.61353 / 0.32 (22796) SS BOND : bond 0.00716 / 0.38 ( 1) SS BOND : angle 1.58463 / 0.83 ( 2) hydrogen bonds : bond 0.02996 / 2.03 ( 1036) hydrogen bonds : angle 4.24610 / 3.08 ( 3000) link_TRANS : bond 0.00086 / 0.05 ( 1) link_TRANS : angle 0.24977 / 0.12 ( 3) ********************** 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 262 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9034 (mttt) cc_final: 0.8155 (tmtt) REVERT: A 123 ASN cc_start: 0.9709 (m110) cc_final: 0.9478 (m110) REVERT: A 210 TYR cc_start: 0.7990 (m-10) cc_final: 0.7759 (m-10) REVERT: A 294 TRP cc_start: 0.8905 (p-90) cc_final: 0.8535 (p-90) REVERT: A 296 ASP cc_start: 0.8866 (m-30) cc_final: 0.8646 (m-30) REVERT: A 320 LEU cc_start: 0.9332 (mt) cc_final: 0.9092 (mt) REVERT: A 324 PHE cc_start: 0.9055 (m-80) cc_final: 0.8630 (m-80) REVERT: A 617 ASN cc_start: 0.7320 (t160) cc_final: 0.6782 (t0) REVERT: A 620 MET cc_start: 0.7024 (ttm) cc_final: 0.6796 (mtm) REVERT: A 652 LEU cc_start: 0.9372 (tt) cc_final: 0.8733 (tt) REVERT: A 656 PHE cc_start: 0.9355 (m-80) cc_final: 0.8861 (m-80) REVERT: A 972 TYR cc_start: 0.6327 (t80) cc_final: 0.6102 (t80) REVERT: A 998 ASP cc_start: 0.8342 (m-30) cc_final: 0.7932 (p0) REVERT: A 1125 PHE cc_start: 0.8973 (t80) cc_final: 0.8584 (t80) REVERT: A 1129 MET cc_start: 0.9102 (mmp) cc_final: 0.8778 (mmp) REVERT: A 1137 MET cc_start: 0.7796 (ptt) cc_final: 0.7449 (ppp) REVERT: A 1168 LYS cc_start: 0.8653 (tptp) cc_final: 0.8085 (tmtt) REVERT: A 1189 ILE cc_start: 0.9577 (mt) cc_final: 0.8976 (tp) REVERT: A 1241 MET cc_start: 0.8642 (mmp) cc_final: 0.8427 (tmm) REVERT: A 1365 TYR cc_start: 0.8233 (t80) cc_final: 0.7946 (t80) REVERT: A 1372 ILE cc_start: 0.9709 (mt) cc_final: 0.9455 (mm) REVERT: B 226 MET cc_start: -0.1155 (mmm) cc_final: -0.1398 (mmm) REVERT: B 245 MET cc_start: 0.2668 (ppp) cc_final: 0.1754 (ptt) REVERT: F 271 LEU cc_start: 0.8980 (tt) cc_final: 0.8550 (mt) REVERT: F 299 ASN cc_start: 0.8777 (t0) cc_final: 0.8411 (t0) REVERT: F 474 GLN cc_start: 0.6396 (tt0) cc_final: 0.6168 (mm-40) REVERT: F 571 ASP cc_start: 0.8607 (m-30) cc_final: 0.8248 (m-30) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.1023 time to fit residues: 43.5952 Evaluate side-chains 219 residues out of total 1895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 199 optimal weight: 0.0270 chunk 65 optimal weight: 40.0000 chunk 106 optimal weight: 0.3980 chunk 36 optimal weight: 40.0000 chunk 190 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 62 optimal weight: 40.0000 chunk 85 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 115 optimal weight: 30.0000 overall best weight: 1.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 617 ASN A 654 ASN A 939 GLN ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN F 408 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.131486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.094750 restraints weight = 61822.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.091879 restraints weight = 50112.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.092131 restraints weight = 45332.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.092838 restraints weight = 34134.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.092996 restraints weight = 29773.726| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16663 Z= 0.127 Angle : 0.624 9.028 22801 Z= 0.324 Chirality : 0.039 0.253 2857 Planarity : 0.004 0.059 2999 Dihedral : 4.459 27.699 2589 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 1.76 % Allowed : 9.99 % Favored : 88.25 % Rotamer: Outliers : 0.18 % Allowed : 0.46 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.20), residues: 2103 helix: 1.79 (0.15), residues: 1200 sheet: -2.47 (0.39), residues: 154 loop : -2.58 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 505 TYR 0.017 0.001 TYR A1048 PHE 0.030 0.001 PHE A1376 TRP 0.036 0.002 TRP F 245 HIS 0.018 0.002 HIS F 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (16661) covalent geometry : angle 0.62442 / 0.32 (22796) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 0.32916 / 0.19 ( 2) hydrogen bonds : bond 0.03025 / 2.04 ( 1036) hydrogen bonds : angle 4.24744 / 3.08 ( 3000) link_TRANS : bond 0.00085 / 0.04 ( 1) link_TRANS : angle 0.27379 / 0.13 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2960.94 seconds wall clock time: 51 minutes 25.36 seconds (3085.36 seconds total)