Starting phenix.real_space_refine on Wed Jun 18 06:15:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e59_27907/06_2025/8e59_27907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e59_27907/06_2025/8e59_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e59_27907/06_2025/8e59_27907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e59_27907/06_2025/8e59_27907.map" model { file = "/net/cci-nas-00/data/ceres_data/8e59_27907/06_2025/8e59_27907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e59_27907/06_2025/8e59_27907.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 6 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: 30 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.87, per 1000 atoms: 0.58 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: 5.50 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.51 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: 7.97 Time building geometry restraints manager: 6.37 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 - 23.11: 11509 23.11 - 46.22: 934 46.22 - 69.33: 112 69.33 - 92.44: 36 92.44 - 115.55: 33 Dihedral angle restraints: 12624 sinusoidal: 5307 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 12621 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 48.050 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 17.557 115.546 7858 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (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 TRP 0.016 0.001 TRP A1199 HIS 0.002 0.000 HIS A 886 PHE 0.022 0.001 PHE D 686 TYR 0.014 0.001 TYR D1068 ARG 0.003 0.000 ARG A 993 Details of bonding type rmsd link_NAG-ASN : bond 0.01351 ( 6) link_NAG-ASN : angle 5.24707 ( 18) link_BETA1-4 : bond 0.00863 ( 8) link_BETA1-4 : angle 2.77284 ( 24) hydrogen bonds : bond 0.21047 ( 971) hydrogen bonds : angle 6.69207 ( 2823) SS BOND : bond 0.00330 ( 10) SS BOND : angle 1.16202 ( 20) covalent geometry : bond 0.00317 (20742) covalent geometry : angle 0.53518 (28090) Misc. bond : bond 0.00001 ( 1) *********************** 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 : 2.271 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: 0.3176 time to fit residues: 137.4195 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 : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 5.9990 chunk 188 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 127 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 145 optimal weight: 0.7980 chunk 226 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 258 GLN A 273 HIS D 652 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.213264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161911 restraints weight = 21526.171| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.38 r_work: 0.3319 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20767 Z= 0.128 Angle : 0.578 10.597 28152 Z= 0.284 Chirality : 0.044 0.567 3199 Planarity : 0.004 0.052 3554 Dihedral : 10.999 104.099 3043 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.27 % Rotamer: Outliers : 1.45 % Allowed : 12.99 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2472 helix: 1.20 (0.15), residues: 1222 sheet: 0.03 (0.33), residues: 254 loop : -1.22 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.003 0.001 HIS C 94 PHE 0.023 0.001 PHE A1147 TYR 0.014 0.001 TYR A 921 ARG 0.003 0.000 ARG D 843 Details of bonding type rmsd link_NAG-ASN : bond 0.01255 ( 6) link_NAG-ASN : angle 4.99014 ( 18) link_BETA1-4 : bond 0.00744 ( 8) link_BETA1-4 : angle 2.64935 ( 24) hydrogen bonds : bond 0.04455 ( 971) hydrogen bonds : angle 4.57303 ( 2823) SS BOND : bond 0.00227 ( 10) SS BOND : angle 0.78873 ( 20) covalent geometry : bond 0.00277 (20742) covalent geometry : angle 0.55913 (28090) Misc. bond : bond 0.00020 ( 1) *********************** 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 311 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 2.165 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7232 (ptpt) cc_final: 0.6625 (ptmm) REVERT: A 248 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8694 (tt) REVERT: A 297 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.7059 (mmt) REVERT: A 890 ASN cc_start: 0.6664 (m110) cc_final: 0.6183 (m110) REVERT: A 1143 MET cc_start: 0.8694 (mtp) cc_final: 0.8445 (mmt) REVERT: D 34 LYS cc_start: 0.7538 (mtpp) cc_final: 0.7306 (tptt) REVERT: D 506 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7705 (pp) REVERT: D 724 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7929 (tppt) REVERT: D 737 ASP cc_start: 0.8348 (m-30) cc_final: 0.7860 (m-30) REVERT: D 745 PRO cc_start: 0.7100 (Cg_exo) cc_final: 0.6726 (Cg_endo) REVERT: D 747 GLU cc_start: 0.6877 (mp0) cc_final: 0.5594 (tt0) REVERT: C 195 MET cc_start: 0.3175 (mpp) cc_final: 0.2965 (mpp) outliers start: 32 outliers final: 16 residues processed: 298 average time/residue: 0.3062 time to fit residues: 145.9913 Evaluate side-chains 279 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 260 time to evaluate : 2.332 ------------------------------------------------------------------------------- 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 877 GLU 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 D residue 1071 CYS 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 201 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 235 optimal weight: 30.0000 chunk 116 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4308 r_free = 0.4308 target = 0.211757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.164970 restraints weight = 22215.196| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.83 r_work: 0.3236 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1105 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= 0.128 Angle : 0.556 12.255 28152 Z= 0.270 Chirality : 0.043 0.448 3199 Planarity : 0.004 0.049 3554 Dihedral : 9.510 101.927 3043 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 2.04 % Allowed : 14.03 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2472 helix: 1.34 (0.15), residues: 1215 sheet: 0.12 (0.32), residues: 243 loop : -1.20 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 185 HIS 0.002 0.001 HIS A 544 PHE 0.019 0.001 PHE A1147 TYR 0.015 0.001 TYR D1068 ARG 0.006 0.000 ARG D 704 Details of bonding type rmsd link_NAG-ASN : bond 0.01145 ( 6) link_NAG-ASN : angle 4.73825 ( 18) link_BETA1-4 : bond 0.00817 ( 8) link_BETA1-4 : angle 2.77383 ( 24) hydrogen bonds : bond 0.03999 ( 971) hydrogen bonds : angle 4.26861 ( 2823) SS BOND : bond 0.00244 ( 10) SS BOND : angle 0.90271 ( 20) covalent geometry : bond 0.00292 (20742) covalent geometry : angle 0.53677 (28090) Misc. bond : bond 0.00014 ( 1) *********************** 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 322 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 2.734 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7178 (ptpt) cc_final: 0.6584 (ptmm) REVERT: A 248 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8685 (tt) REVERT: A 297 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.6797 (mmt) REVERT: A 890 ASN cc_start: 0.6848 (m110) cc_final: 0.6386 (m110) REVERT: A 923 ASP cc_start: 0.7525 (m-30) cc_final: 0.7317 (m-30) REVERT: A 1026 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: D 34 LYS cc_start: 0.7588 (mtpp) cc_final: 0.7320 (tptt) REVERT: D 506 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7646 (pp) REVERT: D 704 ARG cc_start: 0.8512 (tpt90) cc_final: 0.8043 (tpt90) REVERT: D 708 ASP cc_start: 0.7238 (m-30) cc_final: 0.6365 (m-30) REVERT: D 745 PRO cc_start: 0.7107 (Cg_exo) cc_final: 0.6790 (Cg_endo) REVERT: C 320 MET cc_start: 0.4139 (tmm) cc_final: 0.3848 (tmm) outliers start: 45 outliers final: 27 residues processed: 304 average time/residue: 0.3266 time to fit residues: 161.2824 Evaluate side-chains 284 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 2.687 ------------------------------------------------------------------------------- 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 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 639 LEU Chi-restraints excluded: chain A residue 1026 GLN 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 220 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.211041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.163327 restraints weight = 22143.652| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.87 r_work: 0.3236 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20767 Z= 0.120 Angle : 0.554 12.377 28152 Z= 0.267 Chirality : 0.042 0.297 3199 Planarity : 0.003 0.051 3554 Dihedral : 8.503 100.946 3043 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.27 % Rotamer: Outliers : 2.17 % Allowed : 15.07 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2472 helix: 1.39 (0.15), residues: 1217 sheet: -0.02 (0.32), residues: 253 loop : -1.18 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1103 HIS 0.003 0.000 HIS A 886 PHE 0.020 0.001 PHE A1147 TYR 0.013 0.001 TYR D1068 ARG 0.003 0.000 ARG A 993 Details of bonding type rmsd link_NAG-ASN : bond 0.00962 ( 6) link_NAG-ASN : angle 5.09073 ( 18) link_BETA1-4 : bond 0.00839 ( 8) link_BETA1-4 : angle 2.76777 ( 24) hydrogen bonds : bond 0.03548 ( 971) hydrogen bonds : angle 4.12392 ( 2823) SS BOND : bond 0.00335 ( 10) SS BOND : angle 1.32205 ( 20) covalent geometry : bond 0.00272 (20742) covalent geometry : angle 0.53195 (28090) Misc. bond : bond 0.00007 ( 1) *********************** 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 313 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 265 time to evaluate : 2.053 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7169 (ptpt) cc_final: 0.6586 (ptmm) REVERT: A 248 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8683 (tt) REVERT: A 297 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.6913 (mmt) REVERT: A 639 LEU cc_start: 0.7309 (tp) cc_final: 0.6935 (tp) REVERT: A 890 ASN cc_start: 0.6837 (m110) cc_final: 0.6369 (m110) REVERT: A 959 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.7017 (m-30) REVERT: A 1028 MET cc_start: 0.8505 (mtp) cc_final: 0.8303 (mtm) REVERT: A 1378 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8143 (mtp180) REVERT: D 34 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7335 (tptt) REVERT: D 506 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7675 (pp) REVERT: D 745 PRO cc_start: 0.6949 (Cg_exo) cc_final: 0.6616 (Cg_endo) REVERT: C 320 MET cc_start: 0.3874 (tmm) cc_final: 0.3628 (tmm) outliers start: 48 outliers final: 35 residues processed: 297 average time/residue: 0.2961 time to fit residues: 140.4019 Evaluate side-chains 291 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 2.217 ------------------------------------------------------------------------------- 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 327 THR 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 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 150 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR 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 610 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 740 ILE 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 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 167 optimal weight: 2.9990 chunk 224 optimal weight: 0.1980 chunk 173 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 232 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 122 optimal weight: 0.0000 chunk 27 optimal weight: 5.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS D 41 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.212047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.160452 restraints weight = 21612.193| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.48 r_work: 0.3315 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 20767 Z= 0.101 Angle : 0.526 9.866 28152 Z= 0.256 Chirality : 0.041 0.280 3199 Planarity : 0.003 0.049 3554 Dihedral : 7.792 100.065 3043 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 1.86 % Allowed : 15.75 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2472 helix: 1.52 (0.15), residues: 1216 sheet: -0.03 (0.32), residues: 255 loop : -1.15 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 337 HIS 0.003 0.000 HIS D 864 PHE 0.029 0.001 PHE A1147 TYR 0.012 0.001 TYR D1068 ARG 0.004 0.000 ARG D 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00902 ( 6) link_NAG-ASN : angle 4.70700 ( 18) link_BETA1-4 : bond 0.00867 ( 8) link_BETA1-4 : angle 2.64868 ( 24) hydrogen bonds : bond 0.03278 ( 971) hydrogen bonds : angle 4.00846 ( 2823) SS BOND : bond 0.00309 ( 10) SS BOND : angle 1.49221 ( 20) covalent geometry : bond 0.00218 (20742) covalent geometry : angle 0.50500 (28090) Misc. bond : bond 0.00008 ( 1) *********************** 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 315 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 2.124 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7255 (ptpt) cc_final: 0.6667 (ptmm) REVERT: A 248 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8685 (tt) REVERT: A 297 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.7001 (mmt) REVERT: A 408 GLU cc_start: 0.7636 (tp30) cc_final: 0.7402 (mm-30) REVERT: A 639 LEU cc_start: 0.7336 (tp) cc_final: 0.6954 (tp) REVERT: A 727 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8655 (mm) REVERT: A 890 ASN cc_start: 0.6893 (m110) cc_final: 0.6425 (m110) REVERT: A 923 ASP cc_start: 0.7533 (m-30) cc_final: 0.7327 (m-30) REVERT: A 959 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.7016 (m-30) REVERT: D 34 LYS cc_start: 0.7634 (mtpp) cc_final: 0.7362 (tptt) REVERT: D 40 MET cc_start: 0.7652 (ptm) cc_final: 0.7449 (ptm) REVERT: D 268 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8965 (t) REVERT: D 506 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7861 (pp) REVERT: D 704 ARG cc_start: 0.8608 (tpt90) cc_final: 0.8028 (tpt90) REVERT: D 708 ASP cc_start: 0.7474 (m-30) cc_final: 0.6638 (m-30) REVERT: C 195 MET cc_start: 0.2864 (mpp) cc_final: 0.2520 (mpp) outliers start: 41 outliers final: 25 residues processed: 299 average time/residue: 0.3218 time to fit residues: 153.2108 Evaluate side-chains 289 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 2.008 ------------------------------------------------------------------------------- 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 531 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 727 ILE 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 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 150 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE 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 737 ASP 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 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 207 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 147 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.210075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.162696 restraints weight = 22214.443| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.94 r_work: 0.3266 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 20767 Z= 0.113 Angle : 0.534 9.608 28152 Z= 0.261 Chirality : 0.041 0.260 3199 Planarity : 0.003 0.050 3554 Dihedral : 7.526 99.429 3043 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.55 % Rotamer: Outliers : 2.08 % Allowed : 16.38 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2472 helix: 1.56 (0.15), residues: 1210 sheet: -0.08 (0.32), residues: 257 loop : -1.17 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1103 HIS 0.002 0.000 HIS D 864 PHE 0.026 0.001 PHE A1147 TYR 0.014 0.001 TYR D1068 ARG 0.006 0.000 ARG A1378 Details of bonding type rmsd link_NAG-ASN : bond 0.00861 ( 6) link_NAG-ASN : angle 4.39060 ( 18) link_BETA1-4 : bond 0.00819 ( 8) link_BETA1-4 : angle 2.72408 ( 24) hydrogen bonds : bond 0.03277 ( 971) hydrogen bonds : angle 3.99419 ( 2823) SS BOND : bond 0.00291 ( 10) SS BOND : angle 1.50814 ( 20) covalent geometry : bond 0.00261 (20742) covalent geometry : angle 0.51528 (28090) Misc. bond : bond 0.00012 ( 1) *********************** 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 309 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 2.189 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7154 (ptpt) cc_final: 0.6580 (ptmm) REVERT: A 248 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8703 (tt) REVERT: A 297 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.6745 (mmt) REVERT: A 408 GLU cc_start: 0.7387 (tp30) cc_final: 0.7146 (mm-30) REVERT: A 890 ASN cc_start: 0.6855 (m110) cc_final: 0.6486 (m110) REVERT: A 923 ASP cc_start: 0.7464 (m-30) cc_final: 0.7240 (m-30) REVERT: A 1028 MET cc_start: 0.8753 (mtm) cc_final: 0.8237 (ptt) REVERT: A 1071 VAL cc_start: 0.8850 (p) cc_final: 0.8630 (m) REVERT: D 34 LYS cc_start: 0.7634 (mtpp) cc_final: 0.7324 (tptt) REVERT: D 268 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8900 (t) REVERT: D 499 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.8132 (mtm-85) REVERT: D 506 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7699 (pp) REVERT: D 646 GLU cc_start: 0.7304 (mp0) cc_final: 0.6959 (mp0) REVERT: D 704 ARG cc_start: 0.8519 (tpt90) cc_final: 0.7978 (tpt90) REVERT: D 708 ASP cc_start: 0.7223 (m-30) cc_final: 0.6266 (m-30) REVERT: D 737 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: C 195 MET cc_start: 0.2710 (mpp) cc_final: 0.2431 (mpp) REVERT: C 320 MET cc_start: 0.3731 (tmm) cc_final: 0.3436 (tmm) outliers start: 46 outliers final: 34 residues processed: 296 average time/residue: 0.2903 time to fit residues: 138.1839 Evaluate side-chains 298 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 2.018 ------------------------------------------------------------------------------- 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 530 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 610 MET 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 150 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR 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 610 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 740 ILE 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 221 LEU 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 170 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 224 optimal weight: 30.0000 chunk 128 optimal weight: 0.6980 chunk 236 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 235 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS D 717 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.210749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.164241 restraints weight = 22527.445| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.90 r_work: 0.3243 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 20767 Z= 0.111 Angle : 0.534 10.603 28152 Z= 0.260 Chirality : 0.041 0.260 3199 Planarity : 0.003 0.049 3554 Dihedral : 7.244 98.670 3043 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 2.08 % Allowed : 16.70 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2472 helix: 1.58 (0.15), residues: 1212 sheet: -0.03 (0.32), residues: 257 loop : -1.17 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1103 HIS 0.002 0.000 HIS D 864 PHE 0.025 0.001 PHE A1147 TYR 0.013 0.001 TYR D1068 ARG 0.006 0.000 ARG A1378 Details of bonding type rmsd link_NAG-ASN : bond 0.00873 ( 6) link_NAG-ASN : angle 4.20821 ( 18) link_BETA1-4 : bond 0.00816 ( 8) link_BETA1-4 : angle 2.75507 ( 24) hydrogen bonds : bond 0.03207 ( 971) hydrogen bonds : angle 3.97068 ( 2823) SS BOND : bond 0.00298 ( 10) SS BOND : angle 1.60853 ( 20) covalent geometry : bond 0.00255 (20742) covalent geometry : angle 0.51601 (28090) Misc. bond : bond 0.00010 ( 1) *********************** 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 313 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 2.165 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7094 (ptpt) cc_final: 0.6528 (ptmm) REVERT: A 248 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8706 (tt) REVERT: A 297 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.6788 (mmt) REVERT: A 408 GLU cc_start: 0.7268 (tp30) cc_final: 0.7033 (mm-30) REVERT: A 606 GLU cc_start: 0.6890 (mm-30) cc_final: 0.5481 (mp0) REVERT: A 890 ASN cc_start: 0.6742 (m110) cc_final: 0.6384 (m110) REVERT: A 923 ASP cc_start: 0.7488 (m-30) cc_final: 0.7281 (m-30) REVERT: A 1028 MET cc_start: 0.8761 (mtm) cc_final: 0.8220 (ptt) REVERT: D 34 LYS cc_start: 0.7645 (mtpp) cc_final: 0.7316 (tptt) REVERT: D 268 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8900 (t) REVERT: D 506 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7731 (pp) REVERT: D 646 GLU cc_start: 0.7507 (mp0) cc_final: 0.7156 (mp0) REVERT: D 704 ARG cc_start: 0.8471 (tpt90) cc_final: 0.7990 (tpt90) REVERT: D 708 ASP cc_start: 0.7224 (m-30) cc_final: 0.6243 (m-30) REVERT: D 737 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: C 195 MET cc_start: 0.2779 (mpp) cc_final: 0.2457 (mpp) REVERT: C 320 MET cc_start: 0.3881 (tmm) cc_final: 0.3656 (tmm) REVERT: C 342 LEU cc_start: 0.1142 (tp) cc_final: 0.0765 (mt) outliers start: 46 outliers final: 37 residues processed: 300 average time/residue: 0.3099 time to fit residues: 148.2024 Evaluate side-chains 296 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 254 time to evaluate : 2.940 ------------------------------------------------------------------------------- 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 530 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 610 MET 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 150 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 370 GLN 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 673 SER Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 743 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 55 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 71 optimal weight: 0.0870 chunk 158 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.211753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.156781 restraints weight = 21257.298| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.21 r_work: 0.3170 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 20767 Z= 0.100 Angle : 0.527 9.545 28152 Z= 0.256 Chirality : 0.041 0.262 3199 Planarity : 0.003 0.050 3554 Dihedral : 6.957 97.978 3043 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 2.22 % Allowed : 16.83 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.17), residues: 2472 helix: 1.64 (0.15), residues: 1211 sheet: 0.05 (0.32), residues: 260 loop : -1.16 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1103 HIS 0.002 0.000 HIS D 864 PHE 0.022 0.001 PHE A1147 TYR 0.013 0.001 TYR D1068 ARG 0.005 0.000 ARG A1378 Details of bonding type rmsd link_NAG-ASN : bond 0.00898 ( 6) link_NAG-ASN : angle 4.16957 ( 18) link_BETA1-4 : bond 0.00803 ( 8) link_BETA1-4 : angle 2.75616 ( 24) hydrogen bonds : bond 0.03074 ( 971) hydrogen bonds : angle 3.92741 ( 2823) SS BOND : bond 0.00209 ( 10) SS BOND : angle 1.45955 ( 20) covalent geometry : bond 0.00223 (20742) covalent geometry : angle 0.50886 (28090) Misc. bond : bond 0.00014 ( 1) *********************** 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 313 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 2.041 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7138 (ptpt) cc_final: 0.6504 (ptmm) REVERT: A 248 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8667 (tt) REVERT: A 297 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.6842 (mmt) REVERT: A 408 GLU cc_start: 0.7196 (tp30) cc_final: 0.6966 (mm-30) REVERT: A 606 GLU cc_start: 0.6935 (mm-30) cc_final: 0.5550 (mp0) REVERT: A 727 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8659 (mm) REVERT: A 890 ASN cc_start: 0.6674 (m110) cc_final: 0.6284 (m110) REVERT: A 923 ASP cc_start: 0.7504 (m-30) cc_final: 0.7237 (m-30) REVERT: A 1019 MET cc_start: 0.8173 (mtt) cc_final: 0.7919 (mpp) REVERT: A 1028 MET cc_start: 0.8779 (mtm) cc_final: 0.8111 (ptt) REVERT: A 1071 VAL cc_start: 0.8817 (p) cc_final: 0.8562 (m) REVERT: D 34 LYS cc_start: 0.7473 (mtpp) cc_final: 0.7122 (tptt) REVERT: D 40 MET cc_start: 0.7497 (ptm) cc_final: 0.7251 (ptm) REVERT: D 268 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8881 (t) REVERT: D 506 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7599 (pp) REVERT: D 591 LEU cc_start: 0.8520 (pt) cc_final: 0.8228 (mt) REVERT: D 646 GLU cc_start: 0.7637 (mp0) cc_final: 0.7407 (mp0) REVERT: D 704 ARG cc_start: 0.8382 (tpt90) cc_final: 0.7905 (tpt90) REVERT: D 708 ASP cc_start: 0.7366 (m-30) cc_final: 0.6332 (m-30) REVERT: D 737 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: C 195 MET cc_start: 0.2770 (mpp) cc_final: 0.2491 (mpp) REVERT: C 320 MET cc_start: 0.3901 (tmm) cc_final: 0.3683 (tmm) REVERT: C 342 LEU cc_start: 0.1213 (tp) cc_final: 0.0879 (mt) outliers start: 49 outliers final: 36 residues processed: 295 average time/residue: 0.3027 time to fit residues: 142.1473 Evaluate side-chains 302 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 260 time to evaluate : 2.027 ------------------------------------------------------------------------------- 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 530 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 727 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 150 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR 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 673 SER Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 737 ASP 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 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 156 optimal weight: 3.9990 chunk 115 optimal weight: 0.0170 chunk 182 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.211457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.156571 restraints weight = 23127.137| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 5.14 r_work: 0.3087 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.145 20767 Z= 0.104 Angle : 0.528 9.552 28152 Z= 0.257 Chirality : 0.041 0.263 3199 Planarity : 0.003 0.049 3554 Dihedral : 6.739 96.934 3043 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 2.22 % Allowed : 17.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2472 helix: 1.68 (0.15), residues: 1211 sheet: 0.05 (0.32), residues: 265 loop : -1.17 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1269 HIS 0.002 0.000 HIS D 864 PHE 0.022 0.001 PHE A1147 TYR 0.015 0.001 TYR A 921 ARG 0.005 0.000 ARG A1378 Details of bonding type rmsd link_NAG-ASN : bond 0.00871 ( 6) link_NAG-ASN : angle 4.04773 ( 18) link_BETA1-4 : bond 0.00827 ( 8) link_BETA1-4 : angle 2.80983 ( 24) hydrogen bonds : bond 0.03054 ( 971) hydrogen bonds : angle 3.91086 ( 2823) SS BOND : bond 0.00205 ( 10) SS BOND : angle 1.38885 ( 20) covalent geometry : bond 0.00244 (20742) covalent geometry : angle 0.51040 (28090) Misc. bond : bond 0.00010 ( 1) *********************** 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 309 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 260 time to evaluate : 2.082 Fit side-chains REVERT: A 237 LYS cc_start: 0.7004 (ptpt) cc_final: 0.6364 (ptmm) REVERT: A 248 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8647 (tt) REVERT: A 297 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.6548 (mmt) REVERT: A 408 GLU cc_start: 0.7127 (tp30) cc_final: 0.6901 (mm-30) REVERT: A 606 GLU cc_start: 0.6973 (mm-30) cc_final: 0.5570 (mp0) REVERT: A 727 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8622 (mm) REVERT: A 890 ASN cc_start: 0.6474 (m110) cc_final: 0.6117 (m110) REVERT: A 923 ASP cc_start: 0.7469 (m-30) cc_final: 0.7251 (m-30) REVERT: A 1464 MET cc_start: 0.6908 (ptt) cc_final: 0.6496 (ptm) REVERT: D 34 LYS cc_start: 0.7400 (mtpp) cc_final: 0.7048 (tptt) REVERT: D 43 ASP cc_start: 0.7369 (t0) cc_final: 0.7110 (t0) REVERT: D 268 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8856 (t) REVERT: D 324 ASN cc_start: 0.8580 (t0) cc_final: 0.8310 (t0) REVERT: D 506 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7511 (pp) REVERT: D 591 LEU cc_start: 0.8460 (pt) cc_final: 0.8197 (mt) REVERT: D 595 GLN cc_start: 0.8171 (tp40) cc_final: 0.7916 (tp40) REVERT: D 646 GLU cc_start: 0.7572 (mp0) cc_final: 0.7320 (mp0) REVERT: D 673 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8365 (p) REVERT: D 704 ARG cc_start: 0.8271 (tpt90) cc_final: 0.7728 (tpt90) REVERT: D 708 ASP cc_start: 0.7200 (m-30) cc_final: 0.6013 (m-30) REVERT: D 737 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: C 195 MET cc_start: 0.2627 (mpp) cc_final: 0.2422 (mpp) REVERT: C 342 LEU cc_start: 0.1105 (tp) cc_final: 0.0802 (mt) outliers start: 49 outliers final: 37 residues processed: 292 average time/residue: 0.2978 time to fit residues: 139.9892 Evaluate side-chains 301 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 2.306 ------------------------------------------------------------------------------- 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 636 LEU Chi-restraints excluded: chain A residue 727 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 150 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 370 GLN 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 673 SER Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 743 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 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 138 optimal weight: 0.7980 chunk 234 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 203 optimal weight: 0.0870 chunk 81 optimal weight: 0.9980 chunk 230 optimal weight: 0.0030 chunk 136 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN 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 = 0.212146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.158241 restraints weight = 22964.025| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.35 r_work: 0.3124 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1758 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= 0.100 Angle : 0.530 9.695 28152 Z= 0.256 Chirality : 0.041 0.262 3199 Planarity : 0.003 0.050 3554 Dihedral : 6.591 96.245 3043 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.25 % Favored : 95.71 % Rotamer: Outliers : 1.99 % Allowed : 17.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2472 helix: 1.74 (0.15), residues: 1212 sheet: 0.05 (0.32), residues: 265 loop : -1.15 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 441 HIS 0.002 0.000 HIS D 864 PHE 0.022 0.001 PHE A1147 TYR 0.015 0.001 TYR A 921 ARG 0.005 0.000 ARG A1378 Details of bonding type rmsd link_NAG-ASN : bond 0.00885 ( 6) link_NAG-ASN : angle 3.99350 ( 18) link_BETA1-4 : bond 0.00836 ( 8) link_BETA1-4 : angle 2.77818 ( 24) hydrogen bonds : bond 0.02987 ( 971) hydrogen bonds : angle 3.87638 ( 2823) SS BOND : bond 0.00199 ( 10) SS BOND : angle 1.33491 ( 20) covalent geometry : bond 0.00230 (20742) covalent geometry : angle 0.51342 (28090) Misc. bond : bond 0.00012 ( 1) ********************** 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 306 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 2.030 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7026 (ptpt) cc_final: 0.6395 (ptmm) REVERT: A 248 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8654 (tt) REVERT: A 297 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.6819 (mmt) REVERT: A 408 GLU cc_start: 0.7211 (tp30) cc_final: 0.7000 (mm-30) REVERT: A 606 GLU cc_start: 0.6991 (mm-30) cc_final: 0.5647 (mp0) REVERT: A 890 ASN cc_start: 0.6539 (m110) cc_final: 0.6152 (m110) REVERT: A 923 ASP cc_start: 0.7544 (m-30) cc_final: 0.7277 (m-30) REVERT: A 993 ARG cc_start: 0.7208 (ptt90) cc_final: 0.6967 (ptt90) REVERT: A 1071 VAL cc_start: 0.8839 (p) cc_final: 0.8572 (m) REVERT: A 1150 PHE cc_start: 0.7554 (t80) cc_final: 0.7212 (t80) REVERT: D 34 LYS cc_start: 0.7441 (mtpp) cc_final: 0.7077 (tptt) REVERT: D 43 ASP cc_start: 0.7554 (t0) cc_final: 0.7287 (t0) REVERT: D 268 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8934 (t) REVERT: D 324 ASN cc_start: 0.8651 (t0) cc_final: 0.8403 (t0) REVERT: D 506 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7646 (pp) REVERT: D 591 LEU cc_start: 0.8490 (pt) cc_final: 0.8254 (mt) REVERT: D 595 GLN cc_start: 0.8217 (tp40) cc_final: 0.7945 (tp40) REVERT: D 646 GLU cc_start: 0.7619 (mp0) cc_final: 0.7367 (mp0) REVERT: D 673 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8399 (p) REVERT: D 704 ARG cc_start: 0.8500 (tpt90) cc_final: 0.8027 (tpt90) REVERT: D 708 ASP cc_start: 0.7490 (m-30) cc_final: 0.6376 (m-30) REVERT: D 737 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: C 195 MET cc_start: 0.3159 (mpp) cc_final: 0.2881 (mpp) outliers start: 44 outliers final: 37 residues processed: 292 average time/residue: 0.3003 time to fit residues: 140.6571 Evaluate side-chains 297 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 2.279 ------------------------------------------------------------------------------- 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 636 LEU 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 268 THR 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 673 SER Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 743 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 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 69 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.210270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.161066 restraints weight = 22899.834| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.24 r_work: 0.3075 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 20767 Z= 0.121 Angle : 0.549 9.986 28152 Z= 0.268 Chirality : 0.042 0.260 3199 Planarity : 0.003 0.049 3554 Dihedral : 6.589 94.970 3043 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 2.17 % Allowed : 17.51 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2472 helix: 1.69 (0.15), residues: 1214 sheet: -0.03 (0.32), residues: 265 loop : -1.21 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1103 HIS 0.002 0.000 HIS A 886 PHE 0.023 0.001 PHE A1147 TYR 0.014 0.001 TYR D1068 ARG 0.005 0.000 ARG A1378 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 6) link_NAG-ASN : angle 4.01612 ( 18) link_BETA1-4 : bond 0.00815 ( 8) link_BETA1-4 : angle 2.89619 ( 24) hydrogen bonds : bond 0.03207 ( 971) hydrogen bonds : angle 3.93629 ( 2823) SS BOND : bond 0.00211 ( 10) SS BOND : angle 1.45628 ( 20) covalent geometry : bond 0.00289 (20742) covalent geometry : angle 0.53207 (28090) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13851.92 seconds wall clock time: 237 minutes 1.99 seconds (14221.99 seconds total)