Starting phenix.real_space_refine on Sat Jul 4 12:32:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e59_27907/07_2026/8e59_27907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e59_27907/07_2026/8e59_27907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e59_27907/07_2026/8e59_27907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e59_27907/07_2026/8e59_27907.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8e59_27907/07_2026/8e59_27907.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e59_27907/07_2026/8e59_27907.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e59_27907/07_2026/8e59_27907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e59_27907/07_2026/8e59_27907.map" } resolution = 3.1 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: 7 Type Number sf(0) Gaussians I 2 10.91 5 Ca 2 9.91 5 P 1 5.49 5 S 112 5.16 5 C 13097 2.51 5 N 3350 2.21 5 O 3745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20309 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9900 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {' CA': 1, '3PE': 1, 'BBI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.04, per 1000 atoms: 0.20 Number of scatterers: 20309 At special positions: 0 Unit cell: (172.67, 170.442, 182.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) I 2 52.95 Ca 2 19.99 S 112 16.00 P 1 15.00 O 3745 8.00 N 3350 7.00 C 13097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 326 " distance=2.04 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 333 " distance=2.04 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1055 " distance=2.03 Simple disulfide: pdb=" SG CYS A1421 " - pdb=" SG CYS A1435 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " 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=1, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 1 " - " ASN D 184 " " NAG D1201 " - " ASN D 92 " " NAG E 1 " - " ASN D 348 " " NAG F 1 " - " ASN D 468 " " NAG G 1 " - " ASN D 613 " " NAG H 1 " - " ASN D 895 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 835.4 milliseconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 18 sheets defined 55.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.626A pdb=" N ILE A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 181 removed outlier: 3.636A pdb=" N LYS A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 218 Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.790A pdb=" N ALA A 241 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 243 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 245 " --> pdb=" O PHE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 248 No H-bonds generated for 'chain 'A' and resid 247 through 248' Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.670A pdb=" N GLY A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 293 Processing helix chain 'A' and resid 349 through 362 Processing helix chain 'A' and resid 365 through 377 removed outlier: 3.649A pdb=" N VAL A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.654A pdb=" N TYR A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 420 removed outlier: 3.962A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 431 removed outlier: 3.677A pdb=" N LEU A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 445 removed outlier: 3.559A pdb=" N LYS A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TRP A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 442 " --> pdb=" O TYR A 438 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 541 Processing helix chain 'A' and resid 548 through 575 Processing helix chain 'A' and resid 579 through 585 removed outlier: 4.135A pdb=" N PHE A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 585' Processing helix chain 'A' and resid 585 through 607 removed outlier: 4.010A pdb=" N ARG A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 623 removed outlier: 3.791A pdb=" N VAL A 617 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 636 through 646 removed outlier: 3.644A pdb=" N VAL A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 673 Processing helix chain 'A' and resid 690 through 704 Processing helix chain 'A' and resid 706 through 717 removed outlier: 3.612A pdb=" N VAL A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 728 removed outlier: 4.000A pdb=" N GLY A 725 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N MET A 726 " --> pdb=" O SER A 723 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 727 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 728 " --> pdb=" O GLY A 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 722 through 728' Processing helix chain 'A' and resid 729 through 772 removed outlier: 3.830A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 748 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 749 " --> pdb=" O ASN A 745 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 751 " --> pdb=" O PHE A 747 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 754 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 884 removed outlier: 4.357A pdb=" N LYS A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU A 882 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 904 Processing helix chain 'A' and resid 913 through 942 removed outlier: 3.588A pdb=" N TYR A 924 " --> pdb=" O GLY A 920 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 969 removed outlier: 3.506A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 966 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 987 Processing helix chain 'A' and resid 988 through 995 Proline residue: A 991 - end of helix removed outlier: 3.716A pdb=" N ILE A 995 " --> pdb=" O LEU A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1037 removed outlier: 3.560A pdb=" N GLY A1016 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN A1017 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1086 through 1099 Processing helix chain 'A' and resid 1102 through 1112 removed outlier: 3.542A pdb=" N ASP A1112 " --> pdb=" O TYR A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1127 No H-bonds generated for 'chain 'A' and resid 1125 through 1127' Processing helix chain 'A' and resid 1128 through 1140 removed outlier: 4.205A pdb=" N PHE A1132 " --> pdb=" O ILE A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1159 removed outlier: 3.524A pdb=" N PHE A1147 " --> pdb=" O MET A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1174 removed outlier: 3.891A pdb=" N GLN A1174 " --> pdb=" O ASN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1181 Processing helix chain 'A' and resid 1192 through 1203 removed outlier: 4.245A pdb=" N PHE A1198 " --> pdb=" O TYR A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1223 Processing helix chain 'A' and resid 1230 through 1260 removed outlier: 3.763A pdb=" N VAL A1253 " --> pdb=" O THR A1249 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1266 Processing helix chain 'A' and resid 1267 through 1287 removed outlier: 3.571A pdb=" N PHE A1272 " --> pdb=" O ALA A1268 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A1273 " --> pdb=" O TRP A1269 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A1276 " --> pdb=" O PHE A1272 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A1285 " --> pdb=" O ILE A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1322 removed outlier: 3.766A pdb=" N ARG A1319 " --> pdb=" O ILE A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1331 Processing helix chain 'A' and resid 1335 through 1350 removed outlier: 3.615A pdb=" N LEU A1339 " --> pdb=" O GLY A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1373 Processing helix chain 'A' and resid 1391 through 1405 Processing helix chain 'A' and resid 1407 through 1415 Processing helix chain 'A' and resid 1439 through 1466 removed outlier: 3.524A pdb=" N ASN A1466 " --> pdb=" O VAL A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1471 Processing helix chain 'A' and resid 1478 through 1492 removed outlier: 3.996A pdb=" N LEU A1482 " --> pdb=" O GLY A1478 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR A1492 " --> pdb=" O ILE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1511 Processing helix chain 'A' and resid 1526 through 1534 removed outlier: 3.868A pdb=" N VAL A1532 " --> pdb=" O CYS A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1558 removed outlier: 4.347A pdb=" N LEU A1550 " --> pdb=" O PHE A1546 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE A1551 " --> pdb=" O ASN A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1576 removed outlier: 3.706A pdb=" N ASN A1570 " --> pdb=" O LEU A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1589 removed outlier: 4.295A pdb=" N LYS A1587 " --> pdb=" O LYS A1583 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A1589 " --> pdb=" O SER A1585 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 53 Processing helix chain 'D' and resid 53 through 65 removed outlier: 3.966A pdb=" N TYR D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN D 65 " --> pdb=" O TYR D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 110 removed outlier: 3.552A pdb=" N ARG D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.590A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 4.186A pdb=" N VAL D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.563A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 266 through 281 removed outlier: 3.624A pdb=" N LYS D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 332 through 344 removed outlier: 3.633A pdb=" N PHE D 339 " --> pdb=" O LYS D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.801A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'D' and resid 418 through 423 Processing helix chain 'D' and resid 425 through 431 removed outlier: 4.253A pdb=" N VAL D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 438 removed outlier: 3.672A pdb=" N GLY D 438 " --> pdb=" O MET D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.755A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 565 removed outlier: 3.738A pdb=" N GLU D 565 " --> pdb=" O PHE D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 removed outlier: 3.589A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 647 removed outlier: 3.821A pdb=" N TYR D 644 " --> pdb=" O THR D 640 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 654 removed outlier: 5.668A pdb=" N ASP D 651 " --> pdb=" O LEU D 648 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU D 654 " --> pdb=" O ASP D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 688 removed outlier: 3.541A pdb=" N LEU D 681 " --> pdb=" O THR D 677 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 686 " --> pdb=" O ASN D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 719 removed outlier: 4.018A pdb=" N ILE D 702 " --> pdb=" O ASN D 698 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 710 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 715 " --> pdb=" O PHE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 752 removed outlier: 4.158A pdb=" N ASN D 751 " --> pdb=" O GLU D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 770 Processing helix chain 'D' and resid 817 through 827 Processing helix chain 'D' and resid 865 through 870 removed outlier: 3.616A pdb=" N GLN D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 878 Processing helix chain 'D' and resid 879 through 889 removed outlier: 3.540A pdb=" N HIS D 885 " --> pdb=" O SER D 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 120 through 132 removed outlier: 3.501A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 190 through 208 removed outlier: 4.263A pdb=" N MET C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N MET C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 239 removed outlier: 3.831A pdb=" N ILE C 238 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU C 239 " --> pdb=" O THR C 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 239' Processing helix chain 'C' and resid 246 through 263 removed outlier: 3.722A pdb=" N GLU C 255 " --> pdb=" O GLN C 251 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 296 through 306 removed outlier: 3.851A pdb=" N ARG C 305 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 306 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 314 through 327 Processing helix chain 'C' and resid 329 through 333 Processing helix chain 'C' and resid 341 through 360 removed outlier: 3.538A pdb=" N GLU C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 300 through 303 removed outlier: 3.891A pdb=" N THR A 300 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 334 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1058 through 1062 Processing sheet with id=AA3, first strand: chain 'A' and resid 1499 through 1500 Processing sheet with id=AA4, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AA5, first strand: chain 'D' and resid 122 through 123 removed outlier: 6.478A pdb=" N VAL D 122 " --> pdb=" O GLN D 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.718A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY D 489 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY D 462 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP D 491 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE D 460 " --> pdb=" O ASP D 491 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER D 493 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU D 458 " --> pdb=" O SER D 493 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.718A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY D 489 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY D 462 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP D 491 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE D 460 " --> pdb=" O ASP D 491 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER D 493 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU D 458 " --> pdb=" O SER D 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AA9, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.042A pdb=" N ILE D 256 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE D 294 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL D 258 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU D 255 " --> pdb=" O MET D 359 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE D 361 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU D 257 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE D 358 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE D 387 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL D 389 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR D 362 " --> pdb=" O VAL D 389 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 521 through 523 removed outlier: 3.666A pdb=" N LEU D 523 " --> pdb=" O ALA D 514 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 658 through 661 removed outlier: 4.227A pdb=" N ILE D 740 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR D 736 " --> pdb=" O ILE D 740 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS D 815 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ARG D 732 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLY D 813 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL D 734 " --> pdb=" O VAL D 811 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 811 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 800 through 801 Processing sheet with id=AB4, first strand: chain 'D' and resid 859 through 861 removed outlier: 7.057A pdb=" N LEU D 859 " --> pdb=" O ASP D 854 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP D 854 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET D 861 " --> pdb=" O ILE D 852 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 851 " --> pdb=" O ILE D1016 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU D1019 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 892 through 904 removed outlier: 4.743A pdb=" N GLN D 901 " --> pdb=" O CYS D 974 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N CYS D 974 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D 903 " --> pdb=" O GLN D 972 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN D 972 " --> pdb=" O VAL D 903 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 65 removed outlier: 3.761A pdb=" N LYS C 96 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE C 105 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS C 98 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N TRP C 103 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.999A pdb=" N TYR C 70 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 87 " --> pdb=" O TYR C 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.880A pdb=" N VAL C 292 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 289 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU C 337 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE C 291 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 212 through 215 removed outlier: 3.870A pdb=" N VAL C 268 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR C 215 " --> pdb=" O VAL C 268 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2823 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: 3.74 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 6574 1.37 - 1.52: 10168 1.52 - 1.68: 3822 1.68 - 1.84: 176 1.84 - 1.99: 2 Bond restraints: 20742 Sorted by residual: bond pdb=" CBC BBI A2201 " pdb=" IBD BBI A2201 " ideal model delta sigma weight residual 2.097 1.988 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CAR BBI A2201 " pdb=" IAS BBI A2201 " ideal model delta sigma weight residual 2.098 1.991 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" CAV BBI A2201 " pdb=" CAW BBI A2201 " ideal model delta sigma weight residual 1.510 1.614 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CAW BBI A2201 " pdb=" NAX BBI A2201 " ideal model delta sigma weight residual 1.449 1.534 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 NAG F 3 " pdb=" O5 NAG F 3 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 20737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 27887 2.58 - 5.15: 168 5.15 - 7.73: 29 7.73 - 10.31: 4 10.31 - 12.88: 2 Bond angle restraints: 28090 Sorted by residual: angle pdb=" C TYR D 744 " pdb=" N PRO D 745 " pdb=" CA PRO D 745 " ideal model delta sigma weight residual 119.84 114.19 5.65 1.25e+00 6.40e-01 2.04e+01 angle pdb=" CAM BBI A2201 " pdb=" CAN BBI A2201 " pdb=" CAP BBI A2201 " ideal model delta sigma weight residual 118.51 131.39 -12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" N SER A 252 " pdb=" CA SER A 252 " pdb=" C SER A 252 " ideal model delta sigma weight residual 111.07 106.91 4.16 1.07e+00 8.73e-01 1.51e+01 angle pdb=" CA TYR D 744 " pdb=" C TYR D 744 " pdb=" N PRO D 745 " ideal model delta sigma weight residual 120.52 117.36 3.16 8.30e-01 1.45e+00 1.45e+01 angle pdb=" CAC BBI A2201 " pdb=" CAD BBI A2201 " pdb=" CAE BBI A2201 " ideal model delta sigma weight residual 112.57 123.57 -11.00 3.00e+00 1.11e-01 1.35e+01 ... (remaining 28085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.78: 10970 19.78 - 39.56: 1091 39.56 - 59.35: 190 59.35 - 79.13: 37 79.13 - 98.91: 11 Dihedral angle restraints: 12299 sinusoidal: 4982 harmonic: 7317 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 167.62 -74.62 1 1.00e+01 1.00e-02 7.05e+01 dihedral pdb=" CB CYS A 301 " pdb=" SG CYS A 301 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual -86.00 -149.51 63.51 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS A1421 " pdb=" SG CYS A1421 " pdb=" SG CYS A1435 " pdb=" CB CYS A1435 " ideal model delta sinusoidal sigma weight residual -86.00 -141.43 55.43 1 1.00e+01 1.00e-02 4.15e+01 ... (remaining 12296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 3187 0.138 - 0.276: 9 0.276 - 0.414: 2 0.414 - 0.552: 0 0.552 - 0.690: 1 Chirality restraints: 3199 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 895 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 184 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN D 348 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 3196 not shown) Planarity restraints: 3560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 743 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C VAL D 743 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL D 743 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR D 744 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 140 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO C 141 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 141 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 141 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1416 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A1417 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A1417 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1417 " -0.023 5.00e-02 4.00e+02 ... (remaining 3557 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.67: 286 2.67 - 3.24: 19882 3.24 - 3.82: 34053 3.82 - 4.39: 42226 4.39 - 4.96: 72581 Nonbonded interactions: 169028 Sorted by model distance: nonbonded pdb=" OD1 ASN D 895 " pdb=" O3 NAG H 1 " model vdw 2.098 3.040 nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.247 3.040 nonbonded pdb=" OG SER D 594 " pdb=" O ASP D 596 " model vdw 2.267 3.040 nonbonded pdb=" O THR D 32 " pdb=" OG SER D 35 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASN D 668 " pdb=" OG SER D 696 " model vdw 2.272 3.040 ... (remaining 169023 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } 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 individual isotropic 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.790 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.003 0.109 20767 Z= 0.158 Angle : 0.558 12.885 28152 Z= 0.270 Chirality : 0.042 0.690 3199 Planarity : 0.003 0.051 3554 Dihedral : 15.886 98.909 7533 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 0.54 % Allowed : 12.76 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % 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: -0.04 (0.17), residues: 2472 helix: 1.02 (0.15), residues: 1184 sheet: 0.14 (0.36), residues: 217 loop : -1.25 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 993 TYR 0.014 0.001 TYR D1068 PHE 0.022 0.001 PHE D 686 TRP 0.016 0.001 TRP A1199 HIS 0.002 0.000 HIS A 886 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (20742) covalent geometry : angle 0.53518 / 0.26 (28090) SS BOND : bond 0.00330 / 0.18 ( 10) SS BOND : angle 1.16202 / 0.60 ( 20) hydrogen bonds : bond 0.21047 / 13.83 ( 971) hydrogen bonds : angle 6.69207 / 4.90 ( 2823) Misc. bond : bond 0.00001 / 0.00 ( 1) link_BETA1-4 : bond 0.00863 / 0.53 ( 8) link_BETA1-4 : angle 2.77284 / 1.59 ( 24) link_NAG-ASN : bond 0.01351 / 0.80 ( 6) link_NAG-ASN : angle 5.24707 / 3.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 269 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 606 GLU cc_start: 0.6617 (mm-30) cc_final: 0.5366 (mp0) REVERT: D 745 PRO cc_start: 0.7176 (Cg_exo) cc_final: 0.6883 (Cg_endo) outliers start: 12 outliers final: 0 residues processed: 274 average time/residue: 0.1303 time to fit residues: 56.7586 Evaluate side-chains 255 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 7.9990 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN A 273 HIS D 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.213855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163353 restraints weight = 21354.733| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.24 r_work: 0.3311 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20767 Z= 0.121 Angle : 0.558 11.548 28152 Z= 0.277 Chirality : 0.044 0.694 3199 Planarity : 0.004 0.052 3554 Dihedral : 4.244 60.715 2718 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.27 % Rotamer: Outliers : 1.45 % Allowed : 12.85 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % 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: 0.19 (0.17), residues: 2472 helix: 1.22 (0.15), residues: 1221 sheet: -0.02 (0.33), residues: 256 loop : -1.21 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 993 TYR 0.015 0.001 TYR A 921 PHE 0.023 0.001 PHE A1147 TRP 0.012 0.001 TRP D 36 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (20742) covalent geometry : angle 0.53873 / 0.27 (28090) SS BOND : bond 0.00241 / 0.13 ( 10) SS BOND : angle 0.76659 / 0.39 ( 20) hydrogen bonds : bond 0.04437 / 2.94 ( 971) hydrogen bonds : angle 4.56871 / 3.32 ( 2823) Misc. bond : bond 0.00028 / 0.01 ( 1) link_BETA1-4 : bond 0.00746 / 0.50 ( 8) link_BETA1-4 : angle 2.19529 / 1.24 ( 24) link_NAG-ASN : bond 0.01448 / 0.83 ( 6) link_NAG-ASN : angle 5.18632 / 3.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7216 (ptpt) cc_final: 0.6615 (ptmm) REVERT: A 248 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8677 (tt) REVERT: A 297 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.6988 (mmt) REVERT: A 890 ASN cc_start: 0.6630 (m110) cc_final: 0.6150 (m110) REVERT: A 1143 MET cc_start: 0.8675 (mtp) cc_final: 0.8429 (mmt) REVERT: D 34 LYS cc_start: 0.7534 (mtpp) cc_final: 0.7309 (tptt) REVERT: D 506 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7681 (pp) REVERT: D 724 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7916 (tppt) REVERT: D 737 ASP cc_start: 0.8306 (m-30) cc_final: 0.7801 (m-30) REVERT: D 745 PRO cc_start: 0.7061 (Cg_exo) cc_final: 0.6695 (Cg_endo) REVERT: D 747 GLU cc_start: 0.6806 (mp0) cc_final: 0.5554 (tt0) outliers start: 32 outliers final: 14 residues processed: 300 average time/residue: 0.1303 time to fit residues: 62.7525 Evaluate side-chains 277 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 260 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 221 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 116 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 273 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.211452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163275 restraints weight = 22071.649| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.70 r_work: 0.3237 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20767 Z= 0.115 Angle : 0.526 10.664 28152 Z= 0.259 Chirality : 0.043 0.654 3199 Planarity : 0.003 0.049 3554 Dihedral : 3.958 40.954 2718 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.27 % Rotamer: Outliers : 1.72 % Allowed : 13.94 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % 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: 0.35 (0.17), residues: 2472 helix: 1.36 (0.15), residues: 1222 sheet: 0.18 (0.33), residues: 243 loop : -1.18 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 197 TYR 0.013 0.001 TYR D 764 PHE 0.019 0.001 PHE A1147 TRP 0.011 0.001 TRP D 36 HIS 0.002 0.000 HIS D 864 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (20742) covalent geometry : angle 0.50640 / 0.25 (28090) SS BOND : bond 0.00217 / 0.12 ( 10) SS BOND : angle 0.85231 / 0.44 ( 20) hydrogen bonds : bond 0.03884 / 2.57 ( 971) hydrogen bonds : angle 4.23237 / 3.07 ( 2823) Misc. bond : bond 0.00019 / 0.01 ( 1) link_BETA1-4 : bond 0.00794 / 0.54 ( 8) link_BETA1-4 : angle 2.36900 / 1.37 ( 24) link_NAG-ASN : bond 0.01388 / 0.80 ( 6) link_NAG-ASN : angle 4.94327 / 3.66 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7111 (ptpt) cc_final: 0.6511 (ptmm) REVERT: A 248 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8665 (tt) REVERT: A 297 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.6706 (mmt) REVERT: A 890 ASN cc_start: 0.6572 (m110) cc_final: 0.6104 (m110) REVERT: A 1028 MET cc_start: 0.8437 (mtp) cc_final: 0.8223 (mtm) REVERT: A 1207 PHE cc_start: 0.5434 (t80) cc_final: 0.5223 (t80) REVERT: D 34 LYS cc_start: 0.7477 (mtpp) cc_final: 0.7239 (tptt) REVERT: D 506 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7604 (pp) REVERT: D 704 ARG cc_start: 0.8464 (tpt90) cc_final: 0.7959 (tpt90) REVERT: D 708 ASP cc_start: 0.7170 (m-30) cc_final: 0.6287 (m-30) REVERT: D 745 PRO cc_start: 0.7047 (Cg_exo) cc_final: 0.6698 (Cg_endo) REVERT: D 1003 PHE cc_start: 0.8396 (p90) cc_final: 0.8175 (p90) REVERT: C 195 MET cc_start: 0.3246 (mpp) cc_final: 0.2883 (mpp) REVERT: C 320 MET cc_start: 0.3727 (tmm) cc_final: 0.3453 (tmm) outliers start: 38 outliers final: 20 residues processed: 293 average time/residue: 0.1376 time to fit residues: 64.9199 Evaluate side-chains 277 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 254 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 866 ASP Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 219 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 165 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.212079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164779 restraints weight = 22276.310| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.76 r_work: 0.3270 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20767 Z= 0.123 Angle : 0.535 10.902 28152 Z= 0.262 Chirality : 0.043 0.646 3199 Planarity : 0.003 0.051 3554 Dihedral : 3.934 41.503 2718 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.27 % Rotamer: Outliers : 1.81 % Allowed : 15.25 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % 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: 0.38 (0.17), residues: 2472 helix: 1.42 (0.15), residues: 1218 sheet: 0.01 (0.32), residues: 253 loop : -1.15 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 993 TYR 0.013 0.001 TYR D1068 PHE 0.020 0.001 PHE A1147 TRP 0.010 0.001 TRP A1103 HIS 0.002 0.000 HIS A 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (20742) covalent geometry : angle 0.51428 / 0.26 (28090) SS BOND : bond 0.00388 / 0.21 ( 10) SS BOND : angle 1.43684 / 0.76 ( 20) hydrogen bonds : bond 0.03577 / 2.36 ( 971) hydrogen bonds : angle 4.10439 / 2.96 ( 2823) Misc. bond : bond 0.00012 / 0.01 ( 1) link_BETA1-4 : bond 0.00807 / 0.56 ( 8) link_BETA1-4 : angle 2.39634 / 1.38 ( 24) link_NAG-ASN : bond 0.01355 / 0.78 ( 6) link_NAG-ASN : angle 4.95585 / 3.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7161 (ptpt) cc_final: 0.6579 (ptmm) REVERT: A 248 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8693 (tt) REVERT: A 297 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.6842 (mmt) REVERT: A 639 LEU cc_start: 0.7291 (tp) cc_final: 0.6938 (tp) REVERT: A 890 ASN cc_start: 0.6678 (m110) cc_final: 0.6220 (m110) REVERT: A 959 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.7002 (m-30) REVERT: D 34 LYS cc_start: 0.7617 (mtpp) cc_final: 0.7341 (tptt) REVERT: D 506 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7653 (pp) REVERT: D 704 ARG cc_start: 0.8437 (tpt90) cc_final: 0.7871 (tpt90) REVERT: D 708 ASP cc_start: 0.7124 (m-30) cc_final: 0.5980 (m-30) REVERT: D 745 PRO cc_start: 0.6962 (Cg_exo) cc_final: 0.6623 (Cg_endo) REVERT: C 195 MET cc_start: 0.2764 (mpp) cc_final: 0.2435 (mpp) REVERT: C 320 MET cc_start: 0.3898 (tmm) cc_final: 0.3646 (tmm) outliers start: 40 outliers final: 30 residues processed: 294 average time/residue: 0.1392 time to fit residues: 65.8201 Evaluate side-chains 294 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 224 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 HIS D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.212319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.166100 restraints weight = 22309.264| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.76 r_work: 0.3248 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20767 Z= 0.115 Angle : 0.532 11.014 28152 Z= 0.261 Chirality : 0.043 0.632 3199 Planarity : 0.003 0.049 3554 Dihedral : 3.894 41.939 2718 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.19 % Rotamer: Outliers : 1.99 % Allowed : 15.70 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % 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: 0.41 (0.17), residues: 2472 helix: 1.48 (0.15), residues: 1217 sheet: -0.06 (0.32), residues: 255 loop : -1.16 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1378 TYR 0.013 0.001 TYR D1068 PHE 0.021 0.001 PHE A1147 TRP 0.011 0.001 TRP A1103 HIS 0.003 0.000 HIS D 864 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (20742) covalent geometry : angle 0.51253 / 0.26 (28090) SS BOND : bond 0.00263 / 0.14 ( 10) SS BOND : angle 1.60362 / 0.81 ( 20) hydrogen bonds : bond 0.03415 / 2.26 ( 971) hydrogen bonds : angle 4.03719 / 2.90 ( 2823) Misc. bond : bond 0.00009 / 0.00 ( 1) link_BETA1-4 : bond 0.00818 / 0.59 ( 8) link_BETA1-4 : angle 2.34415 / 1.36 ( 24) link_NAG-ASN : bond 0.01313 / 0.75 ( 6) link_NAG-ASN : angle 4.75217 / 3.59 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7143 (ptpt) cc_final: 0.6562 (ptmm) REVERT: A 248 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8682 (tt) REVERT: A 297 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.6819 (mmt) REVERT: A 375 ASP cc_start: 0.8483 (m-30) cc_final: 0.8248 (m-30) REVERT: A 639 LEU cc_start: 0.7286 (tp) cc_final: 0.6912 (tp) REVERT: A 890 ASN cc_start: 0.6676 (m110) cc_final: 0.6215 (m110) REVERT: A 959 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6996 (m-30) REVERT: A 1028 MET cc_start: 0.8705 (mtm) cc_final: 0.8243 (ptt) REVERT: D 34 LYS cc_start: 0.7597 (mtpp) cc_final: 0.7340 (tptt) REVERT: D 506 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7640 (pp) REVERT: C 195 MET cc_start: 0.2752 (mpp) cc_final: 0.2462 (mpp) outliers start: 44 outliers final: 31 residues processed: 299 average time/residue: 0.1305 time to fit residues: 63.1634 Evaluate side-chains 293 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 89 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 237 optimal weight: 0.0060 chunk 190 optimal weight: 6.9990 chunk 243 optimal weight: 0.2980 chunk 231 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.211927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.158634 restraints weight = 22602.385| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.18 r_work: 0.3126 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 20767 Z= 0.101 Angle : 0.521 11.022 28152 Z= 0.255 Chirality : 0.042 0.609 3199 Planarity : 0.003 0.050 3554 Dihedral : 3.760 41.677 2718 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 1.72 % Allowed : 16.52 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % 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: 0.49 (0.17), residues: 2472 helix: 1.58 (0.15), residues: 1216 sheet: -0.01 (0.31), residues: 260 loop : -1.17 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1378 TYR 0.014 0.001 TYR D1068 PHE 0.018 0.001 PHE D 686 TRP 0.011 0.001 TRP A1103 HIS 0.003 0.000 HIS D 864 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (20742) covalent geometry : angle 0.50167 / 0.25 (28090) SS BOND : bond 0.00251 / 0.14 ( 10) SS BOND : angle 1.60273 / 0.81 ( 20) hydrogen bonds : bond 0.03169 / 2.10 ( 971) hydrogen bonds : angle 3.94903 / 2.84 ( 2823) Misc. bond : bond 0.00009 / 0.00 ( 1) link_BETA1-4 : bond 0.00812 / 0.56 ( 8) link_BETA1-4 : angle 2.26933 / 1.31 ( 24) link_NAG-ASN : bond 0.01365 / 0.80 ( 6) link_NAG-ASN : angle 4.74879 / 3.60 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7023 (ptpt) cc_final: 0.6379 (ptmm) REVERT: A 248 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8637 (tt) REVERT: A 332 GLU cc_start: 0.7712 (pt0) cc_final: 0.7345 (pm20) REVERT: A 375 ASP cc_start: 0.8630 (m-30) cc_final: 0.8404 (m-30) REVERT: A 408 GLU cc_start: 0.7316 (tp30) cc_final: 0.7087 (mm-30) REVERT: A 890 ASN cc_start: 0.6640 (m110) cc_final: 0.6249 (m110) REVERT: A 959 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6667 (m-30) REVERT: A 1028 MET cc_start: 0.8792 (mtm) cc_final: 0.8084 (ptt) REVERT: D 34 LYS cc_start: 0.7428 (mtpp) cc_final: 0.7059 (tptt) REVERT: D 88 LYS cc_start: 0.8804 (tptp) cc_final: 0.8596 (tptp) REVERT: D 499 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.8275 (mtm-85) REVERT: D 506 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7581 (pp) REVERT: D 591 LEU cc_start: 0.8455 (pt) cc_final: 0.8139 (mt) REVERT: D 646 GLU cc_start: 0.7526 (mp0) cc_final: 0.7223 (mp0) REVERT: D 704 ARG cc_start: 0.8494 (tpt90) cc_final: 0.7997 (tpt90) REVERT: D 708 ASP cc_start: 0.7651 (m-30) cc_final: 0.6749 (m-30) REVERT: C 195 MET cc_start: 0.2727 (mpp) cc_final: 0.2470 (mpp) REVERT: C 320 MET cc_start: 0.4063 (tmm) cc_final: 0.3797 (tmm) outliers start: 38 outliers final: 25 residues processed: 303 average time/residue: 0.1316 time to fit residues: 63.9184 Evaluate side-chains 287 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 866 ASP Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 98 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 143 optimal weight: 0.5980 chunk 182 optimal weight: 0.0980 chunk 112 optimal weight: 10.0000 chunk 106 optimal weight: 0.4980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 273 HIS C 94 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.211456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.157372 restraints weight = 22823.194| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.24 r_work: 0.3104 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 20767 Z= 0.109 Angle : 0.527 11.003 28152 Z= 0.257 Chirality : 0.043 0.611 3199 Planarity : 0.003 0.049 3554 Dihedral : 3.766 41.624 2718 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 1.95 % Allowed : 16.79 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % 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: 0.51 (0.17), residues: 2472 helix: 1.62 (0.15), residues: 1212 sheet: -0.06 (0.31), residues: 267 loop : -1.18 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1378 TYR 0.015 0.001 TYR A 921 PHE 0.019 0.001 PHE D 686 TRP 0.011 0.001 TRP A1103 HIS 0.002 0.000 HIS D 864 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (20742) covalent geometry : angle 0.50792 / 0.25 (28090) SS BOND : bond 0.00202 / 0.12 ( 10) SS BOND : angle 1.63220 / 0.80 ( 20) hydrogen bonds : bond 0.03176 / 2.10 ( 971) hydrogen bonds : angle 3.92750 / 2.82 ( 2823) Misc. bond : bond 0.00007 / 0.00 ( 1) link_BETA1-4 : bond 0.00799 / 0.55 ( 8) link_BETA1-4 : angle 2.31981 / 1.34 ( 24) link_NAG-ASN : bond 0.01369 / 0.82 ( 6) link_NAG-ASN : angle 4.68346 / 3.54 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7067 (ptpt) cc_final: 0.6427 (ptmm) REVERT: A 248 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8660 (tt) REVERT: A 297 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7144 (mmt) REVERT: A 332 GLU cc_start: 0.7689 (pt0) cc_final: 0.7278 (pm20) REVERT: A 375 ASP cc_start: 0.8660 (m-30) cc_final: 0.8437 (m-30) REVERT: A 408 GLU cc_start: 0.7311 (tp30) cc_final: 0.7060 (mm-30) REVERT: A 606 GLU cc_start: 0.6947 (mm-30) cc_final: 0.5516 (mp0) REVERT: A 890 ASN cc_start: 0.6672 (m110) cc_final: 0.6275 (m110) REVERT: A 959 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6665 (m-30) REVERT: A 1028 MET cc_start: 0.8829 (mtm) cc_final: 0.8133 (ptt) REVERT: A 1071 VAL cc_start: 0.8858 (p) cc_final: 0.8570 (m) REVERT: A 1150 PHE cc_start: 0.7685 (t80) cc_final: 0.7262 (t80) REVERT: D 34 LYS cc_start: 0.7464 (mtpp) cc_final: 0.7104 (tptt) REVERT: D 40 MET cc_start: 0.7574 (ptm) cc_final: 0.7312 (ptm) REVERT: D 88 LYS cc_start: 0.8852 (tptp) cc_final: 0.8643 (tptp) REVERT: D 506 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7618 (pp) REVERT: D 591 LEU cc_start: 0.8501 (pt) cc_final: 0.8189 (mt) REVERT: D 646 GLU cc_start: 0.7500 (mp0) cc_final: 0.7142 (mp0) REVERT: D 704 ARG cc_start: 0.8480 (tpt90) cc_final: 0.7962 (tpt90) REVERT: D 708 ASP cc_start: 0.7573 (m-30) cc_final: 0.6596 (m-30) REVERT: C 195 MET cc_start: 0.2732 (mpp) cc_final: 0.2481 (mpp) REVERT: C 320 MET cc_start: 0.4131 (tmm) cc_final: 0.3907 (tmm) outliers start: 43 outliers final: 31 residues processed: 294 average time/residue: 0.1246 time to fit residues: 58.9325 Evaluate side-chains 296 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 129 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 237 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 115 optimal weight: 0.0040 overall best weight: 1.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.208421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.158676 restraints weight = 22349.683| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.13 r_work: 0.3054 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20767 Z= 0.157 Angle : 0.578 10.956 28152 Z= 0.283 Chirality : 0.045 0.634 3199 Planarity : 0.004 0.050 3554 Dihedral : 4.056 43.486 2718 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.06 % Rotamer: Outliers : 1.99 % Allowed : 17.38 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % 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 (0.17), residues: 2472 helix: 1.49 (0.15), residues: 1216 sheet: -0.07 (0.32), residues: 255 loop : -1.26 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 993 TYR 0.014 0.001 TYR D1068 PHE 0.030 0.001 PHE A1147 TRP 0.011 0.001 TRP A1103 HIS 0.003 0.001 HIS A 886 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (20742) covalent geometry : angle 0.55859 / 0.28 (28090) SS BOND : bond 0.00275 / 0.16 ( 10) SS BOND : angle 1.70964 / 0.84 ( 20) hydrogen bonds : bond 0.03616 / 2.38 ( 971) hydrogen bonds : angle 4.06768 / 2.92 ( 2823) Misc. bond : bond 0.00011 / 0.01 ( 1) link_BETA1-4 : bond 0.00778 / 0.53 ( 8) link_BETA1-4 : angle 2.64568 / 1.56 ( 24) link_NAG-ASN : bond 0.01305 / 0.77 ( 6) link_NAG-ASN : angle 4.80994 / 3.66 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.6972 (ptpt) cc_final: 0.6354 (ptmm) REVERT: A 248 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8667 (tt) REVERT: A 375 ASP cc_start: 0.8656 (m-30) cc_final: 0.8404 (m-30) REVERT: A 408 GLU cc_start: 0.7284 (tp30) cc_final: 0.7035 (mm-30) REVERT: A 606 GLU cc_start: 0.6850 (mm-30) cc_final: 0.5458 (mp0) REVERT: A 890 ASN cc_start: 0.6610 (m110) cc_final: 0.6240 (m110) REVERT: D 34 LYS cc_start: 0.7471 (mtpp) cc_final: 0.7100 (tptt) REVERT: D 40 MET cc_start: 0.7446 (ptm) cc_final: 0.7179 (ptm) REVERT: D 506 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7451 (pp) REVERT: D 646 GLU cc_start: 0.7432 (mp0) cc_final: 0.7067 (mp0) REVERT: D 673 SER cc_start: 0.8909 (p) cc_final: 0.8451 (p) REVERT: D 704 ARG cc_start: 0.8412 (tpt90) cc_final: 0.7741 (tpt90) REVERT: D 708 ASP cc_start: 0.7440 (m-30) cc_final: 0.6349 (m-30) REVERT: C 195 MET cc_start: 0.2954 (mpp) cc_final: 0.2646 (mpp) REVERT: C 320 MET cc_start: 0.4142 (tmm) cc_final: 0.3921 (tmm) outliers start: 44 outliers final: 35 residues processed: 288 average time/residue: 0.1241 time to fit residues: 57.8242 Evaluate side-chains 291 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1103 TRP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 93 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 191 optimal weight: 0.5980 chunk 220 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 228 optimal weight: 0.7980 chunk 219 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.207664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.152524 restraints weight = 22312.331| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.21 r_work: 0.3111 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 20767 Z= 0.111 Angle : 0.537 11.042 28152 Z= 0.263 Chirality : 0.043 0.597 3199 Planarity : 0.003 0.049 3554 Dihedral : 3.896 43.337 2718 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 1.86 % Allowed : 17.74 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % 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: 0.46 (0.17), residues: 2472 helix: 1.57 (0.15), residues: 1214 sheet: -0.06 (0.32), residues: 257 loop : -1.18 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1378 TYR 0.013 0.001 TYR A 921 PHE 0.039 0.001 PHE A1147 TRP 0.014 0.001 TRP A1269 HIS 0.002 0.000 HIS D 864 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (20742) covalent geometry : angle 0.51793 / 0.26 (28090) SS BOND : bond 0.00257 / 0.15 ( 10) SS BOND : angle 1.47072 / 0.73 ( 20) hydrogen bonds : bond 0.03260 / 2.16 ( 971) hydrogen bonds : angle 3.99340 / 2.87 ( 2823) Misc. bond : bond 0.00008 / 0.00 ( 1) link_BETA1-4 : bond 0.00843 / 0.59 ( 8) link_BETA1-4 : angle 2.34941 / 1.37 ( 24) link_NAG-ASN : bond 0.01356 / 0.79 ( 6) link_NAG-ASN : angle 4.83106 / 3.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7022 (ptpt) cc_final: 0.6393 (ptmm) REVERT: A 248 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8628 (tt) REVERT: A 375 ASP cc_start: 0.8670 (m-30) cc_final: 0.8424 (m-30) REVERT: A 408 GLU cc_start: 0.7284 (tp30) cc_final: 0.7070 (mm-30) REVERT: A 606 GLU cc_start: 0.6867 (mm-30) cc_final: 0.5411 (mp0) REVERT: A 890 ASN cc_start: 0.6678 (m110) cc_final: 0.6224 (m110) REVERT: A 1028 MET cc_start: 0.8696 (mtm) cc_final: 0.8080 (ptt) REVERT: A 1071 VAL cc_start: 0.8840 (p) cc_final: 0.8556 (m) REVERT: D 34 LYS cc_start: 0.7432 (mtpp) cc_final: 0.7059 (tptt) REVERT: D 40 MET cc_start: 0.7449 (ptm) cc_final: 0.7191 (ptm) REVERT: D 43 ASP cc_start: 0.7523 (t0) cc_final: 0.7254 (t0) REVERT: D 506 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7575 (pp) REVERT: D 646 GLU cc_start: 0.7677 (mp0) cc_final: 0.7411 (mp0) REVERT: D 704 ARG cc_start: 0.8431 (tpt90) cc_final: 0.7926 (tpt90) REVERT: D 708 ASP cc_start: 0.7510 (m-30) cc_final: 0.6507 (m-30) REVERT: D 714 GLU cc_start: 0.8514 (tp30) cc_final: 0.8299 (tp30) REVERT: C 195 MET cc_start: 0.2788 (mpp) cc_final: 0.2522 (mpp) REVERT: C 320 MET cc_start: 0.4171 (tmm) cc_final: 0.3958 (tmm) outliers start: 41 outliers final: 36 residues processed: 287 average time/residue: 0.1257 time to fit residues: 58.0415 Evaluate side-chains 289 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 1103 TRP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 73 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 186 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.210301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.154454 restraints weight = 22711.282| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 4.20 r_work: 0.3097 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 20767 Z= 0.115 Angle : 0.547 10.971 28152 Z= 0.267 Chirality : 0.043 0.595 3199 Planarity : 0.003 0.050 3554 Dihedral : 3.851 43.591 2718 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 2.04 % Allowed : 17.83 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % 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: 0.46 (0.17), residues: 2472 helix: 1.58 (0.15), residues: 1214 sheet: -0.06 (0.32), residues: 255 loop : -1.21 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1378 TYR 0.013 0.001 TYR A 921 PHE 0.035 0.001 PHE A1147 TRP 0.011 0.001 TRP A1103 HIS 0.002 0.000 HIS A 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.11 (20742) covalent geometry : angle 0.52795 / 0.26 (28090) SS BOND : bond 0.00223 / 0.13 ( 10) SS BOND : angle 1.45112 / 0.72 ( 20) hydrogen bonds : bond 0.03218 / 2.13 ( 971) hydrogen bonds : angle 3.96924 / 2.85 ( 2823) Misc. bond : bond 0.00012 / 0.01 ( 1) link_BETA1-4 : bond 0.00794 / 0.55 ( 8) link_BETA1-4 : angle 2.39449 / 1.40 ( 24) link_NAG-ASN : bond 0.01334 / 0.78 ( 6) link_NAG-ASN : angle 4.78407 / 3.60 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.6982 (ptpt) cc_final: 0.6346 (ptmm) REVERT: A 248 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8632 (tt) REVERT: A 375 ASP cc_start: 0.8670 (m-30) cc_final: 0.8430 (m-30) REVERT: A 606 GLU cc_start: 0.6869 (mm-30) cc_final: 0.5463 (mp0) REVERT: A 890 ASN cc_start: 0.6496 (m110) cc_final: 0.6137 (m110) REVERT: A 1028 MET cc_start: 0.8741 (mtm) cc_final: 0.8111 (ptt) REVERT: A 1150 PHE cc_start: 0.7594 (t80) cc_final: 0.7353 (t80) REVERT: A 1469 TYR cc_start: 0.5944 (t80) cc_final: 0.5730 (t80) REVERT: D 34 LYS cc_start: 0.7423 (mtpp) cc_final: 0.7048 (tptt) REVERT: D 43 ASP cc_start: 0.7570 (t0) cc_final: 0.7305 (t0) REVERT: D 506 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7618 (pp) REVERT: D 646 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: D 704 ARG cc_start: 0.8425 (tpt90) cc_final: 0.7959 (tpt90) REVERT: D 708 ASP cc_start: 0.7489 (m-30) cc_final: 0.6389 (m-30) REVERT: D 714 GLU cc_start: 0.8536 (tp30) cc_final: 0.8335 (tp30) REVERT: C 195 MET cc_start: 0.2803 (mpp) cc_final: 0.2537 (mpp) REVERT: C 320 MET cc_start: 0.4154 (tmm) cc_final: 0.3943 (tmm) outliers start: 45 outliers final: 39 residues processed: 279 average time/residue: 0.1357 time to fit residues: 61.2268 Evaluate side-chains 289 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1103 TRP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 646 GLU Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 2.9990 chunk 2 optimal weight: 0.0040 chunk 122 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 226 optimal weight: 0.0170 chunk 99 optimal weight: 0.8980 chunk 234 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 overall best weight: 0.5230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 HIS D 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.212075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.162893 restraints weight = 22750.453| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.03 r_work: 0.3142 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.123 20767 Z= 0.101 Angle : 0.527 10.984 28152 Z= 0.256 Chirality : 0.042 0.573 3199 Planarity : 0.003 0.049 3554 Dihedral : 3.718 42.695 2718 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 1.86 % Allowed : 18.05 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % 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: 0.59 (0.17), residues: 2472 helix: 1.69 (0.15), residues: 1212 sheet: -0.00 (0.32), residues: 260 loop : -1.15 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 704 TYR 0.013 0.001 TYR A 921 PHE 0.039 0.001 PHE A1147 TRP 0.012 0.001 TRP A1103 HIS 0.001 0.000 HIS A 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (20742) covalent geometry : angle 0.50823 / 0.25 (28090) SS BOND : bond 0.00213 / 0.12 ( 10) SS BOND : angle 1.32020 / 0.66 ( 20) hydrogen bonds : bond 0.03037 / 2.01 ( 971) hydrogen bonds : angle 3.89173 / 2.80 ( 2823) Misc. bond : bond 0.00008 / 0.00 ( 1) link_BETA1-4 : bond 0.00808 / 0.55 ( 8) link_BETA1-4 : angle 2.22859 / 1.30 ( 24) link_NAG-ASN : bond 0.01335 / 0.78 ( 6) link_NAG-ASN : angle 4.70277 / 3.56 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6801.57 seconds wall clock time: 116 minutes 28.49 seconds (6988.49 seconds total)