Starting phenix.real_space_refine on Sat Feb 7 03:11:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u61_63894/02_2026/9u61_63894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u61_63894/02_2026/9u61_63894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u61_63894/02_2026/9u61_63894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u61_63894/02_2026/9u61_63894.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u61_63894/02_2026/9u61_63894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u61_63894/02_2026/9u61_63894.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ni 1 6.56 5 S 135 5.16 5 C 18338 2.51 5 N 5005 2.21 5 O 5522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29001 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 4033 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 509, 4029 Classifications: {'peptide': 509} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 489} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 509, 4029 Classifications: {'peptide': 509} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 489} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 4106 Chain: "D" Number of atoms: 7936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7936 Classifications: {'peptide': 992} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 949} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 11977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1541, 11977 Classifications: {'peptide': 1541} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 80, 'TRANS': 1458} Chain breaks: 6 Chain: "C" Number of atoms: 4920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 4920 Classifications: {'peptide': 632} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 594} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' NI': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.89, per 1000 atoms: 0.24 Number of scatterers: 29001 At special positions: 0 Unit cell: (171, 127.3, 201.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ni 1 28.00 S 135 16.00 O 5522 8.00 N 5005 7.00 C 18338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 581 " distance=2.04 Simple disulfide: pdb=" SG CYS B 492 " - pdb=" SG CYS B 508 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 600 " distance=2.03 Simple disulfide: pdb=" SG CYS B 638 " - pdb=" SG CYS B 665 " distance=2.03 Simple disulfide: pdb=" SG CYS B 675 " - pdb=" SG CYS B 705 " distance=2.03 Simple disulfide: pdb=" SG CYS D 693 " - pdb=" SG CYS D 720 " distance=2.03 Simple disulfide: pdb=" SG CYS D 694 " - pdb=" SG CYS D 727 " distance=2.03 Simple disulfide: pdb=" SG CYS D 707 " - pdb=" SG CYS D 728 " distance=2.03 Simple disulfide: pdb=" SG CYS D1101 " - pdb=" SG CYS D1158 " distance=2.03 Simple disulfide: pdb=" SG CYS D1358 " - pdb=" SG CYS D1489 " distance=2.03 Simple disulfide: pdb=" SG CYS D1389 " - pdb=" SG CYS D1458 " distance=2.03 Simple disulfide: pdb=" SG CYS D1506 " - pdb=" SG CYS D1511 " distance=2.04 Simple disulfide: pdb=" SG CYS D1518 " - pdb=" SG CYS D1590 " distance=2.03 Simple disulfide: pdb=" SG CYS D1537 " - pdb=" SG CYS D1661 " distance=2.03 Simple disulfide: pdb=" SG CYS D1637 " - pdb=" SG CYS D1646 " distance=2.04 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 567 " - pdb=" SG CYS E 820 " distance=2.03 Simple disulfide: pdb=" SG CYS E1394 " - pdb=" SG CYS E1566 " distance=2.03 Simple disulfide: pdb=" SG CYS E1471 " - pdb=" SG CYS E1535 " distance=2.03 Simple disulfide: pdb=" SG CYS E1583 " - pdb=" SG CYS E1588 " distance=2.03 Simple disulfide: pdb=" SG CYS E1595 " - pdb=" SG CYS E1673 " distance=2.03 Simple disulfide: pdb=" SG CYS E1618 " - pdb=" SG CYS E1742 " distance=2.03 Simple disulfide: pdb=" SG CYS E1718 " - pdb=" SG CYS E1727 " distance=2.03 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 662 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 1 " - " ASN B 621 " " NAG B 801 " - " ASN B 471 " " NAG C1701 " - " ASN C 85 " " NAG E1801 " - " ASN E 862 " " NAG E1802 " - " ASN E 226 " " NAG F 1 " - " ASN B 467 " Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6870 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 48 sheets defined 22.6% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'B' and resid 266 through 285 removed outlier: 3.645A pdb=" N ILE B 272 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE B 284 " --> pdb=" O MET B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.723A pdb=" N SER B 313 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG B 314 " --> pdb=" O ASP B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 314' Processing helix chain 'B' and resid 315 through 326 Processing helix chain 'B' and resid 339 through 358 removed outlier: 4.068A pdb=" N GLN B 353 " --> pdb=" O MET B 349 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 removed outlier: 4.284A pdb=" N ALA B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 395 " --> pdb=" O HIS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.503A pdb=" N LEU B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 424 " --> pdb=" O TRP B 420 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 451 removed outlier: 3.562A pdb=" N LEU B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS B 451 " --> pdb=" O GLN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 505 through 509 removed outlier: 4.207A pdb=" N CYS B 508 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 509 " --> pdb=" O ALA B 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 505 through 509' Processing helix chain 'B' and resid 585 through 593 Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 633 through 640 removed outlier: 4.215A pdb=" N SER B 637 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 659 removed outlier: 3.981A pdb=" N VAL B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 743 removed outlier: 3.704A pdb=" N GLN B 741 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS B 742 " --> pdb=" O TRP B 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 683 removed outlier: 3.587A pdb=" N VAL D 683 " --> pdb=" O ARG D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 698 removed outlier: 3.662A pdb=" N CYS D 694 " --> pdb=" O LEU D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 711 Processing helix chain 'D' and resid 712 through 714 No H-bonds generated for 'chain 'D' and resid 712 through 714' Processing helix chain 'D' and resid 717 through 743 removed outlier: 3.954A pdb=" N ARG D 740 " --> pdb=" O ARG D 736 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA D 741 " --> pdb=" O GLN D 737 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS D 743 " --> pdb=" O ALA D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 995 removed outlier: 3.506A pdb=" N THR D 991 " --> pdb=" O VAL D 987 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 995 " --> pdb=" O THR D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 996 through 1001 removed outlier: 4.276A pdb=" N LYS D1001 " --> pdb=" O ALA D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1004 No H-bonds generated for 'chain 'D' and resid 1002 through 1004' Processing helix chain 'D' and resid 1012 through 1017 removed outlier: 3.654A pdb=" N ILE D1016 " --> pdb=" O GLN D1013 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D1017 " --> pdb=" O ASN D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1032 Processing helix chain 'D' and resid 1033 through 1038 Processing helix chain 'D' and resid 1040 through 1057 removed outlier: 4.328A pdb=" N GLY D1044 " --> pdb=" O GLU D1040 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D1057 " --> pdb=" O TYR D1053 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1060 No H-bonds generated for 'chain 'D' and resid 1058 through 1060' Processing helix chain 'D' and resid 1075 through 1089 Processing helix chain 'D' and resid 1096 through 1110 removed outlier: 3.619A pdb=" N LEU D1100 " --> pdb=" O ASP D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1131 Processing helix chain 'D' and resid 1132 through 1135 removed outlier: 3.758A pdb=" N ASN D1135 " --> pdb=" O GLY D1132 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1132 through 1135' Processing helix chain 'D' and resid 1136 through 1154 removed outlier: 3.927A pdb=" N ASP D1140 " --> pdb=" O ASN D1136 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D1153 " --> pdb=" O ILE D1149 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1179 removed outlier: 3.668A pdb=" N ALA D1178 " --> pdb=" O ASP D1174 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN D1179 " --> pdb=" O PHE D1175 " (cutoff:3.500A) Processing helix chain 'D' and resid 1185 through 1200 removed outlier: 3.815A pdb=" N MET D1199 " --> pdb=" O ALA D1195 " (cutoff:3.500A) Processing helix chain 'D' and resid 1204 through 1213 Processing helix chain 'D' and resid 1225 through 1243 Processing helix chain 'D' and resid 1248 through 1259 removed outlier: 4.094A pdb=" N VAL D1252 " --> pdb=" O PHE D1248 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D1259 " --> pdb=" O TRP D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1269 through 1286 Processing helix chain 'D' and resid 1414 through 1424 removed outlier: 3.508A pdb=" N GLY D1424 " --> pdb=" O GLN D1420 " (cutoff:3.500A) Processing helix chain 'D' and resid 1510 through 1515 removed outlier: 4.488A pdb=" N CYS D1513 " --> pdb=" O LEU D1510 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D1514 " --> pdb=" O CYS D1511 " (cutoff:3.500A) Processing helix chain 'D' and resid 1528 through 1536 Processing helix chain 'D' and resid 1590 through 1595 removed outlier: 3.839A pdb=" N LYS D1595 " --> pdb=" O ARG D1591 " (cutoff:3.500A) Processing helix chain 'D' and resid 1633 through 1637 Processing helix chain 'D' and resid 1639 through 1659 Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 315 through 326 removed outlier: 3.665A pdb=" N PHE E 319 " --> pdb=" O SER E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 333 Processing helix chain 'E' and resid 534 through 538 removed outlier: 3.765A pdb=" N ALA E 538 " --> pdb=" O HIS E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 610 Processing helix chain 'E' and resid 620 through 629 removed outlier: 3.639A pdb=" N VAL E 624 " --> pdb=" O ASN E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 632 No H-bonds generated for 'chain 'E' and resid 630 through 632' Processing helix chain 'E' and resid 642 through 651 Processing helix chain 'E' and resid 768 through 772 removed outlier: 3.538A pdb=" N ASP E 771 " --> pdb=" O ASP E 768 " (cutoff:3.500A) Processing helix chain 'E' and resid 1000 through 1004 Processing helix chain 'E' and resid 1012 through 1026 Proline residue: E1020 - end of helix removed outlier: 3.708A pdb=" N ALA E1023 " --> pdb=" O ALA E1019 " (cutoff:3.500A) Processing helix chain 'E' and resid 1040 through 1060 removed outlier: 3.751A pdb=" N ASP E1047 " --> pdb=" O ASP E1043 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU E1048 " --> pdb=" O HIS E1044 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE E1056 " --> pdb=" O GLY E1052 " (cutoff:3.500A) Processing helix chain 'E' and resid 1075 through 1085 removed outlier: 3.742A pdb=" N VAL E1085 " --> pdb=" O PHE E1081 " (cutoff:3.500A) Processing helix chain 'E' and resid 1099 through 1110 removed outlier: 3.782A pdb=" N THR E1103 " --> pdb=" O LYS E1099 " (cutoff:3.500A) Processing helix chain 'E' and resid 1137 through 1152 removed outlier: 4.004A pdb=" N ALA E1148 " --> pdb=" O PHE E1144 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS E1151 " --> pdb=" O ILE E1147 " (cutoff:3.500A) Processing helix chain 'E' and resid 1164 through 1186 removed outlier: 3.585A pdb=" N SER E1173 " --> pdb=" O GLU E1169 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU E1179 " --> pdb=" O ALA E1175 " (cutoff:3.500A) Processing helix chain 'E' and resid 1189 through 1203 Processing helix chain 'E' and resid 1206 through 1220 removed outlier: 3.783A pdb=" N ASN E1215 " --> pdb=" O GLY E1211 " (cutoff:3.500A) Processing helix chain 'E' and resid 1261 through 1276 removed outlier: 3.633A pdb=" N THR E1265 " --> pdb=" O TRP E1261 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU E1270 " --> pdb=" O ALA E1266 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU E1273 " --> pdb=" O LEU E1269 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU E1274 " --> pdb=" O LEU E1270 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS E1275 " --> pdb=" O HIS E1271 " (cutoff:3.500A) Processing helix chain 'E' and resid 1279 through 1292 removed outlier: 3.641A pdb=" N ASP E1283 " --> pdb=" O ALA E1279 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN E1292 " --> pdb=" O TRP E1288 " (cutoff:3.500A) Processing helix chain 'E' and resid 1293 through 1295 No H-bonds generated for 'chain 'E' and resid 1293 through 1295' Processing helix chain 'E' and resid 1301 through 1320 removed outlier: 4.305A pdb=" N VAL E1306 " --> pdb=" O THR E1302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP E1310 " --> pdb=" O VAL E1306 " (cutoff:3.500A) Processing helix chain 'E' and resid 1497 through 1506 removed outlier: 4.116A pdb=" N LEU E1504 " --> pdb=" O ASP E1500 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR E1505 " --> pdb=" O LEU E1501 " (cutoff:3.500A) Processing helix chain 'E' and resid 1611 through 1619 Processing helix chain 'E' and resid 1714 through 1720 removed outlier: 3.832A pdb=" N SER E1720 " --> pdb=" O ARG E1716 " (cutoff:3.500A) Processing helix chain 'E' and resid 1720 through 1725 Processing helix chain 'E' and resid 1727 through 1740 removed outlier: 3.810A pdb=" N GLN E1735 " --> pdb=" O ASN E1731 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E1736 " --> pdb=" O ASP E1732 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY E1738 " --> pdb=" O LEU E1734 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 305 through 311 removed outlier: 3.787A pdb=" N VAL C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 320 removed outlier: 3.501A pdb=" N LEU C 319 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 320 " --> pdb=" O GLU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 436 removed outlier: 3.585A pdb=" N GLU C 435 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN C 436 " --> pdb=" O GLU C 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 432 through 436' Processing helix chain 'C' and resid 483 through 487 removed outlier: 3.878A pdb=" N ILE C 487 " --> pdb=" O GLU C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 526 removed outlier: 3.518A pdb=" N PHE C 525 " --> pdb=" O THR C 522 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE C 526 " --> pdb=" O THR C 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 522 through 526' Processing helix chain 'C' and resid 600 through 606 removed outlier: 3.790A pdb=" N LEU C 605 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 removed outlier: 3.826A pdb=" N VAL C 619 " --> pdb=" O LYS C 615 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 620 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 642 removed outlier: 3.582A pdb=" N PHE C 639 " --> pdb=" O TYR C 635 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 642 " --> pdb=" O VAL C 638 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 245 through 246 removed outlier: 6.843A pdb=" N ILE B 245 " --> pdb=" O ASP B 454 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 302 through 304 Processing sheet with id=AA3, first strand: chain 'B' and resid 531 through 533 removed outlier: 3.673A pdb=" N CYS B 492 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 537 " --> pdb=" O LYS B 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 612 through 618 Processing sheet with id=AA5, first strand: chain 'B' and resid 663 through 666 removed outlier: 6.358A pdb=" N ILE B 730 " --> pdb=" O VAL B 697 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 697 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 683 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 771 through 777 removed outlier: 5.414A pdb=" N LEU D 772 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA C 597 " --> pdb=" O LEU D 772 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN D 774 " --> pdb=" O LEU C 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 771 through 777 removed outlier: 5.414A pdb=" N LEU D 772 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA C 597 " --> pdb=" O LEU D 772 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN D 774 " --> pdb=" O LEU C 595 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 787 through 794 Processing sheet with id=AA9, first strand: chain 'D' and resid 829 through 834 removed outlier: 3.765A pdb=" N SER D 892 " --> pdb=" O ASN D 853 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 829 through 834 Processing sheet with id=AB2, first strand: chain 'D' and resid 838 through 840 removed outlier: 3.538A pdb=" N LEU D 866 " --> pdb=" O HIS D 882 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N HIS D 882 " --> pdb=" O LEU D 866 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 936 through 947 removed outlier: 6.785A pdb=" N VAL D1344 " --> pdb=" O VAL D 942 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL D 944 " --> pdb=" O LEU D1342 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU D1342 " --> pdb=" O VAL D 944 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR D 946 " --> pdb=" O GLY D1340 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY D1340 " --> pdb=" O THR D 946 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 957 through 962 removed outlier: 3.843A pdb=" N THR D1331 " --> pdb=" O GLN D1299 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D1307 " --> pdb=" O LEU D1298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1361 through 1369 removed outlier: 3.667A pdb=" N ASN D1382 " --> pdb=" O GLN D1465 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 1431 through 1434 removed outlier: 3.726A pdb=" N LYS D1431 " --> pdb=" O TYR D1447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D1476 " --> pdb=" O SER D1406 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1611 through 1612 removed outlier: 3.933A pdb=" N SER D1619 " --> pdb=" O TRP D1612 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D1551 " --> pdb=" O ILE D1562 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA D1564 " --> pdb=" O LEU D1549 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU D1549 " --> pdb=" O ALA D1564 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLU D1566 " --> pdb=" O THR D1547 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR D1547 " --> pdb=" O GLU D1566 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR D1568 " --> pdb=" O TYR D1545 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR D1545 " --> pdb=" O THR D1568 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS D1570 " --> pdb=" O TYR D1543 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR D1543 " --> pdb=" O LYS D1570 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS D1600 " --> pdb=" O LEU D1549 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N HIS D1601 " --> pdb=" O TRP D1631 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP D1631 " --> pdb=" O HIS D1601 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU D1603 " --> pdb=" O GLU D1629 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D1629 " --> pdb=" O LEU D1603 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP D1605 " --> pdb=" O TRP D1627 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP D1627 " --> pdb=" O TRP D1605 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 87 removed outlier: 7.898A pdb=" N SER E 38 " --> pdb=" O PRO E 28 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 30 through 32 removed outlier: 6.076A pdb=" N VAL E 31 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 140 through 145 Processing sheet with id=AC2, first strand: chain 'E' and resid 149 through 150 removed outlier: 4.004A pdb=" N ARG E 187 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG E 187 " --> pdb=" O GLU E1355 " (cutoff:3.500A) removed outlier: 11.927A pdb=" N GLU E1357 " --> pdb=" O ARG E 187 " (cutoff:3.500A) removed outlier: 15.768A pdb=" N LYS E 189 " --> pdb=" O GLU E1357 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU E1356 " --> pdb=" O VAL E 978 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL E 978 " --> pdb=" O GLU E1356 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR E1383 " --> pdb=" O PHE E 974 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER E 976 " --> pdb=" O LEU E1381 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU E1381 " --> pdb=" O SER E 976 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL E 978 " --> pdb=" O LYS E1379 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS E1379 " --> pdb=" O VAL E 978 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL E 980 " --> pdb=" O THR E1377 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR E1377 " --> pdb=" O VAL E 980 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 241 through 247 Processing sheet with id=AC4, first strand: chain 'E' and resid 252 through 253 removed outlier: 5.871A pdb=" N ILE E 252 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL E 340 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER E 359 " --> pdb=" O LEU E 338 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU E 338 " --> pdb=" O SER E 359 " (cutoff:3.500A) removed outlier: 11.439A pdb=" N GLY E 278 " --> pdb=" O GLN E 302 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N GLN E 302 " --> pdb=" O GLY E 278 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N ALA E 280 " --> pdb=" O GLU E 300 " (cutoff:3.500A) removed outlier: 9.557A pdb=" N GLU E 300 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 10.642A pdb=" N VAL E 282 " --> pdb=" O GLY E 298 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLY E 298 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N PHE E 284 " --> pdb=" O PHE E 296 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 367 through 370 Processing sheet with id=AC6, first strand: chain 'E' and resid 417 through 424 removed outlier: 3.539A pdb=" N GLU E 443 " --> pdb=" O SER E 410 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 475 through 476 Processing sheet with id=AC8, first strand: chain 'E' and resid 514 through 522 removed outlier: 5.190A pdb=" N ILE E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N SER E 511 " --> pdb=" O ILE E 515 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE E 517 " --> pdb=" O ILE E 509 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N HIS E 504 " --> pdb=" O TYR E 548 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N TYR E 548 " --> pdb=" O HIS E 504 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 572 through 574 Processing sheet with id=AD1, first strand: chain 'E' and resid 580 through 581 removed outlier: 3.806A pdb=" N ARG E 785 " --> pdb=" O LEU E 601 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA E 603 " --> pdb=" O LEU E 783 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU E 783 " --> pdb=" O ALA E 603 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASP E 605 " --> pdb=" O ASN E 781 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASN E 781 " --> pdb=" O ASP E 605 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 580 through 581 Processing sheet with id=AD3, first strand: chain 'E' and resid 833 through 836 Processing sheet with id=AD4, first strand: chain 'E' and resid 850 through 851 Processing sheet with id=AD5, first strand: chain 'E' and resid 884 through 889 Processing sheet with id=AD6, first strand: chain 'E' and resid 1339 through 1346 Processing sheet with id=AD7, first strand: chain 'E' and resid 1397 through 1405 removed outlier: 3.718A pdb=" N GLN E1398 " --> pdb=" O TRP E1473 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER E1464 " --> pdb=" O GLN E1542 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN E1542 " --> pdb=" O SER E1464 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E1470 " --> pdb=" O VAL E1536 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E1536 " --> pdb=" O VAL E1470 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E1534 " --> pdb=" O ILE E1472 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 1515 through 1518 removed outlier: 4.409A pdb=" N SER E1553 " --> pdb=" O THR E1489 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 1581 through 1584 Processing sheet with id=AE1, first strand: chain 'E' and resid 1701 through 1702 removed outlier: 3.678A pdb=" N ARG E1633 " --> pdb=" O GLU E1644 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS E1646 " --> pdb=" O VAL E1631 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL E1631 " --> pdb=" O LYS E1646 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR E1648 " --> pdb=" O VAL E1629 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL E1629 " --> pdb=" O THR E1648 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL E1650 " --> pdb=" O PHE E1627 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE E1627 " --> pdb=" O VAL E1650 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS E1652 " --> pdb=" O TYR E1625 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR E1625 " --> pdb=" O HIS E1652 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR E1625 " --> pdb=" O GLY E1687 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 89 Processing sheet with id=AE3, first strand: chain 'C' and resid 33 through 35 removed outlier: 4.067A pdb=" N SER C 70 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 129 through 134 Processing sheet with id=AE5, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.608A pdb=" N GLY C 202 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL C 163 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER C 179 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL C 165 " --> pdb=" O GLN C 177 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN C 177 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 167 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 233 through 238 Processing sheet with id=AE7, first strand: chain 'C' and resid 243 through 244 removed outlier: 5.880A pdb=" N TYR C 243 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU C 324 " --> pdb=" O GLY C 345 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 243 through 244 removed outlier: 5.880A pdb=" N TYR C 243 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU C 324 " --> pdb=" O GLY C 345 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AF1, first strand: chain 'C' and resid 363 through 364 removed outlier: 3.721A pdb=" N VAL C 391 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 397 " --> pdb=" O VAL C 391 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 455 through 459 Processing sheet with id=AF3, first strand: chain 'C' and resid 499 through 507 removed outlier: 4.988A pdb=" N LEU C 500 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN C 496 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C 502 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TYR C 489 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THR C 536 " --> pdb=" O TYR C 489 " (cutoff:3.500A) 1153 hydrogen bonds defined for protein. 3198 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: 7.39 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8172 1.33 - 1.46: 7670 1.46 - 1.59: 13536 1.59 - 1.72: 3 1.72 - 1.85: 212 Bond restraints: 29593 Sorted by residual: bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.599 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CA PHE C 62 " pdb=" C PHE C 62 " ideal model delta sigma weight residual 1.522 1.489 0.033 9.10e-03 1.21e+04 1.33e+01 bond pdb=" C CYS D1661 " pdb=" N PRO D1662 " ideal model delta sigma weight residual 1.332 1.372 -0.040 1.12e-02 7.97e+03 1.26e+01 bond pdb=" CA PRO B 724 " pdb=" C PRO B 724 " ideal model delta sigma weight residual 1.517 1.547 -0.030 9.30e-03 1.16e+04 1.05e+01 bond pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.399 1.463 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 29588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 39716 3.65 - 7.29: 336 7.29 - 10.94: 44 10.94 - 14.58: 8 14.58 - 18.23: 3 Bond angle restraints: 40107 Sorted by residual: angle pdb=" N TYR E1620 " pdb=" CA TYR E1620 " pdb=" C TYR E1620 " ideal model delta sigma weight residual 110.13 102.56 7.57 1.15e+00 7.56e-01 4.33e+01 angle pdb=" N PRO B 724 " pdb=" CA PRO B 724 " pdb=" C PRO B 724 " ideal model delta sigma weight residual 110.70 118.70 -8.00 1.22e+00 6.72e-01 4.30e+01 angle pdb=" N PRO B 723 " pdb=" CA PRO B 723 " pdb=" C PRO B 723 " ideal model delta sigma weight residual 110.70 118.42 -7.72 1.22e+00 6.72e-01 4.00e+01 angle pdb=" CG1 ILE E 127 " pdb=" CB ILE E 127 " pdb=" CG2 ILE E 127 " ideal model delta sigma weight residual 110.70 92.47 18.23 3.00e+00 1.11e-01 3.69e+01 angle pdb=" C PHE D1248 " pdb=" N VAL D1249 " pdb=" CA VAL D1249 " ideal model delta sigma weight residual 120.33 125.02 -4.69 8.00e-01 1.56e+00 3.43e+01 ... (remaining 40102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.64: 16597 25.64 - 51.27: 1374 51.27 - 76.91: 139 76.91 - 102.55: 30 102.55 - 128.18: 3 Dihedral angle restraints: 18143 sinusoidal: 7497 harmonic: 10646 Sorted by residual: dihedral pdb=" CB CYS E1595 " pdb=" SG CYS E1595 " pdb=" SG CYS E1673 " pdb=" CB CYS E1673 " ideal model delta sinusoidal sigma weight residual 93.00 -176.72 -90.28 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS D1637 " pdb=" SG CYS D1637 " pdb=" SG CYS D1646 " pdb=" CB CYS D1646 " ideal model delta sinusoidal sigma weight residual 93.00 -176.91 -90.09 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CA ARG E1300 " pdb=" C ARG E1300 " pdb=" N SER E1301 " pdb=" CA SER E1301 " ideal model delta harmonic sigma weight residual 180.00 141.13 38.87 0 5.00e+00 4.00e-02 6.04e+01 ... (remaining 18140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 4434 0.130 - 0.260: 96 0.260 - 0.389: 9 0.389 - 0.519: 0 0.519 - 0.649: 1 Chirality restraints: 4540 Sorted by residual: chirality pdb=" CA ARG E 791 " pdb=" N ARG E 791 " pdb=" C ARG E 791 " pdb=" CB ARG E 791 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CB VAL C 576 " pdb=" CA VAL C 576 " pdb=" CG1 VAL C 576 " pdb=" CG2 VAL C 576 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA PRO B 723 " pdb=" N PRO B 723 " pdb=" C PRO B 723 " pdb=" CB PRO B 723 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 4537 not shown) Planarity restraints: 5196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 722 " -0.108 5.00e-02 4.00e+02 1.63e-01 4.25e+01 pdb=" N PRO B 723 " 0.282 5.00e-02 4.00e+02 pdb=" CA PRO B 723 " -0.088 5.00e-02 4.00e+02 pdb=" CD PRO B 723 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E1034 " -0.051 2.00e-02 2.50e+03 4.06e-02 4.13e+01 pdb=" CG TRP E1034 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 TRP E1034 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP E1034 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E1034 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP E1034 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E1034 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E1034 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP E1034 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E1034 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 420 " -0.023 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP B 420 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP B 420 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 420 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 420 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 420 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 420 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 420 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 420 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 420 " -0.003 2.00e-02 2.50e+03 ... (remaining 5193 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 472 2.68 - 3.23: 23151 3.23 - 3.79: 41458 3.79 - 4.34: 55856 4.34 - 4.90: 95545 Nonbonded interactions: 216482 Sorted by model distance: nonbonded pdb=" OG1 THR B 337 " pdb="NI NI B 802 " model vdw 2.119 2.180 nonbonded pdb=" OG SER B 264 " pdb="NI NI B 802 " model vdw 2.268 2.180 nonbonded pdb=" O SER C 182 " pdb=" OG SER C 182 " model vdw 2.281 3.040 nonbonded pdb=" O LYS D1209 " pdb=" OG1 THR D1213 " model vdw 2.285 3.040 nonbonded pdb=" O GLY E1011 " pdb=" OG1 THR E1014 " model vdw 2.285 3.040 ... (remaining 216477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.26 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 28.060 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.005 0.139 29627 Z= 0.227 Angle : 0.918 18.229 40185 Z= 0.498 Chirality : 0.054 0.649 4540 Planarity : 0.008 0.163 5190 Dihedral : 17.527 128.183 11201 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 0.53 % Allowed : 26.23 % Favored : 73.24 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.13), residues: 3652 helix: -2.48 (0.15), residues: 648 sheet: 0.90 (0.15), residues: 1195 loop : -2.11 (0.12), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D1512 TYR 0.043 0.002 TYR E1619 PHE 0.027 0.002 PHE D 920 TRP 0.106 0.003 TRP E1034 HIS 0.031 0.001 HIS D1289 Details of bonding type rmsd covalent geometry : bond 0.00466 (29593) covalent geometry : angle 0.91540 (40107) SS BOND : bond 0.00350 ( 24) SS BOND : angle 1.66352 ( 48) hydrogen bonds : bond 0.21902 ( 1114) hydrogen bonds : angle 7.69455 ( 3198) link_ALPHA1-3 : bond 0.01131 ( 1) link_ALPHA1-3 : angle 0.98584 ( 3) link_BETA1-4 : bond 0.00845 ( 3) link_BETA1-4 : angle 2.14785 ( 9) link_NAG-ASN : bond 0.00338 ( 6) link_NAG-ASN : angle 2.27745 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 253 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: B 724 PRO cc_start: 0.7010 (Cg_exo) cc_final: 0.6664 (Cg_endo) REVERT: D 1625 ASP cc_start: 0.7953 (m-30) cc_final: 0.7751 (t0) REVERT: E 863 LEU cc_start: 0.8574 (mt) cc_final: 0.8320 (mp) REVERT: E 1220 MET cc_start: 0.4920 (mtt) cc_final: 0.3692 (tpp) REVERT: E 1686 MET cc_start: 0.7177 (mtp) cc_final: 0.6976 (mtp) outliers start: 17 outliers final: 8 residues processed: 265 average time/residue: 0.1854 time to fit residues: 79.1585 Evaluate side-chains 242 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 234 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 723 PRO Chi-restraints excluded: chain D residue 819 ASP Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 1013 GLN Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 771 ASP Chi-restraints excluded: chain E residue 1633 ARG Chi-restraints excluded: chain C residue 301 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN D 857 ASN D1033 GLN ** D1289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS ** E 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1706 ASN C 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103816 restraints weight = 49559.647| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.21 r_work: 0.3055 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 29627 Z= 0.190 Angle : 0.635 11.232 40185 Z= 0.331 Chirality : 0.046 0.179 4540 Planarity : 0.006 0.149 5190 Dihedral : 6.384 66.937 4197 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 2.48 % Allowed : 24.98 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 3652 helix: -0.90 (0.19), residues: 690 sheet: 1.00 (0.15), residues: 1228 loop : -1.94 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1512 TYR 0.016 0.002 TYR C 209 PHE 0.019 0.002 PHE C 475 TRP 0.030 0.002 TRP B 420 HIS 0.006 0.001 HIS E 834 Details of bonding type rmsd covalent geometry : bond 0.00467 (29593) covalent geometry : angle 0.63130 (40107) SS BOND : bond 0.00322 ( 24) SS BOND : angle 1.29391 ( 48) hydrogen bonds : bond 0.04685 ( 1114) hydrogen bonds : angle 5.50467 ( 3198) link_ALPHA1-3 : bond 0.01558 ( 1) link_ALPHA1-3 : angle 2.38283 ( 3) link_BETA1-4 : bond 0.00517 ( 3) link_BETA1-4 : angle 1.81373 ( 9) link_NAG-ASN : bond 0.00289 ( 6) link_NAG-ASN : angle 1.94211 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 243 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: B 420 TRP cc_start: 0.7689 (t60) cc_final: 0.7322 (t60) REVERT: B 649 PHE cc_start: 0.6278 (m-10) cc_final: 0.6010 (m-10) REVERT: D 927 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8172 (mtpt) REVERT: D 1037 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6049 (m-80) REVERT: E 43 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8854 (tt) REVERT: E 1034 TRP cc_start: 0.6039 (m100) cc_final: 0.5804 (m100) REVERT: E 1120 LEU cc_start: 0.1927 (OUTLIER) cc_final: 0.1522 (tp) REVERT: E 1389 MET cc_start: 0.6164 (tpt) cc_final: 0.5852 (mpp) REVERT: E 1412 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: E 1597 ARG cc_start: 0.6044 (tpp-160) cc_final: 0.5734 (tpp-160) REVERT: E 1613 ARG cc_start: 0.6981 (mtm180) cc_final: 0.6623 (mpp80) REVERT: E 1620 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.6200 (t80) outliers start: 79 outliers final: 45 residues processed: 307 average time/residue: 0.2025 time to fit residues: 99.1160 Evaluate side-chains 276 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 857 ASN Chi-restraints excluded: chain D residue 927 LYS Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1308 THR Chi-restraints excluded: chain D residue 1347 MET Chi-restraints excluded: chain D residue 1430 SER Chi-restraints excluded: chain D residue 1494 HIS Chi-restraints excluded: chain D residue 1519 PHE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 781 ASN Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain E residue 1031 THR Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1119 ASP Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1210 ARG Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1361 SER Chi-restraints excluded: chain E residue 1410 THR Chi-restraints excluded: chain E residue 1412 GLU Chi-restraints excluded: chain E residue 1504 LEU Chi-restraints excluded: chain E residue 1563 GLU Chi-restraints excluded: chain E residue 1620 TYR Chi-restraints excluded: chain E residue 1631 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 638 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 146 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 254 optimal weight: 30.0000 chunk 147 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN B 551 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1289 HIS D1553 GLN E 100 HIS ** E 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1222 GLN ** E1723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.151150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099974 restraints weight = 56695.229| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.14 r_work: 0.2991 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.132 29627 Z= 0.314 Angle : 0.740 13.270 40185 Z= 0.383 Chirality : 0.050 0.202 4540 Planarity : 0.006 0.146 5190 Dihedral : 6.103 55.015 4182 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.13 % Rotamer: Outliers : 4.68 % Allowed : 23.22 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 3652 helix: -0.50 (0.19), residues: 687 sheet: 0.73 (0.14), residues: 1241 loop : -1.95 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E1533 TYR 0.022 0.002 TYR E1027 PHE 0.024 0.002 PHE E 654 TRP 0.027 0.002 TRP B 420 HIS 0.008 0.001 HIS E 834 Details of bonding type rmsd covalent geometry : bond 0.00788 (29593) covalent geometry : angle 0.73378 (40107) SS BOND : bond 0.00560 ( 24) SS BOND : angle 2.33092 ( 48) hydrogen bonds : bond 0.05360 ( 1114) hydrogen bonds : angle 5.44806 ( 3198) link_ALPHA1-3 : bond 0.01642 ( 1) link_ALPHA1-3 : angle 2.95731 ( 3) link_BETA1-4 : bond 0.00266 ( 3) link_BETA1-4 : angle 1.97835 ( 9) link_NAG-ASN : bond 0.00345 ( 6) link_NAG-ASN : angle 2.23087 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 231 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 359 MET cc_start: 0.8137 (tpt) cc_final: 0.7634 (tpp) REVERT: B 420 TRP cc_start: 0.7865 (t60) cc_final: 0.7427 (t60) REVERT: B 586 MET cc_start: 0.8108 (mmm) cc_final: 0.7810 (mmm) REVERT: D 791 MET cc_start: 0.8386 (ttp) cc_final: 0.8176 (ttt) REVERT: D 921 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7670 (tp) REVERT: D 1037 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6261 (m-80) REVERT: D 1465 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: D 1512 ARG cc_start: 0.7836 (mpp-170) cc_final: 0.7229 (mtt90) REVERT: E 43 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8962 (tt) REVERT: E 127 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7180 (mp) REVERT: E 484 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7766 (ttp80) REVERT: E 832 GLU cc_start: 0.8023 (mp0) cc_final: 0.7655 (mp0) REVERT: E 1034 TRP cc_start: 0.6576 (m100) cc_final: 0.5197 (m100) REVERT: E 1043 ASP cc_start: 0.8490 (t70) cc_final: 0.7748 (t70) REVERT: E 1120 LEU cc_start: 0.2016 (OUTLIER) cc_final: 0.1537 (tp) REVERT: E 1373 ASN cc_start: 0.5861 (OUTLIER) cc_final: 0.5497 (p0) REVERT: E 1389 MET cc_start: 0.5716 (tpt) cc_final: 0.5388 (mpp) REVERT: E 1412 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: E 1480 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7792 (mp) REVERT: E 1597 ARG cc_start: 0.6387 (tpp-160) cc_final: 0.6122 (tpp-160) REVERT: E 1620 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6502 (t80) REVERT: E 1706 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.8010 (t0) REVERT: E 1730 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.4909 (mm) REVERT: C 83 MET cc_start: 0.9067 (ttt) cc_final: 0.8401 (ttt) REVERT: C 340 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8698 (mt0) outliers start: 149 outliers final: 81 residues processed: 361 average time/residue: 0.1935 time to fit residues: 112.2006 Evaluate side-chains 313 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 218 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 792 ASN Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1064 SER Chi-restraints excluded: chain D residue 1170 THR Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1324 THR Chi-restraints excluded: chain D residue 1347 MET Chi-restraints excluded: chain D residue 1430 SER Chi-restraints excluded: chain D residue 1465 GLN Chi-restraints excluded: chain D residue 1494 HIS Chi-restraints excluded: chain D residue 1612 TRP Chi-restraints excluded: chain D residue 1625 ASP Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 484 ARG Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 781 ASN Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1027 TYR Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1210 ARG Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1317 ILE Chi-restraints excluded: chain E residue 1361 SER Chi-restraints excluded: chain E residue 1373 ASN Chi-restraints excluded: chain E residue 1410 THR Chi-restraints excluded: chain E residue 1412 GLU Chi-restraints excluded: chain E residue 1415 GLU Chi-restraints excluded: chain E residue 1470 VAL Chi-restraints excluded: chain E residue 1480 LEU Chi-restraints excluded: chain E residue 1504 LEU Chi-restraints excluded: chain E residue 1535 CYS Chi-restraints excluded: chain E residue 1544 VAL Chi-restraints excluded: chain E residue 1563 GLU Chi-restraints excluded: chain E residue 1567 SER Chi-restraints excluded: chain E residue 1620 TYR Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1631 VAL Chi-restraints excluded: chain E residue 1648 THR Chi-restraints excluded: chain E residue 1657 VAL Chi-restraints excluded: chain E residue 1706 ASN Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 333 HIS Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 638 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 272 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 337 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 299 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS ** E 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1723 GLN C 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.154443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103319 restraints weight = 52604.122| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.16 r_work: 0.3038 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 29627 Z= 0.157 Angle : 0.614 16.576 40185 Z= 0.316 Chirality : 0.045 0.355 4540 Planarity : 0.005 0.139 5190 Dihedral : 5.550 44.204 4182 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 3.33 % Allowed : 24.32 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.13), residues: 3652 helix: -0.06 (0.20), residues: 683 sheet: 0.83 (0.15), residues: 1216 loop : -1.85 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1507 TYR 0.016 0.001 TYR E1027 PHE 0.019 0.002 PHE B 649 TRP 0.022 0.001 TRP B 420 HIS 0.004 0.001 HIS B 507 Details of bonding type rmsd covalent geometry : bond 0.00387 (29593) covalent geometry : angle 0.60473 (40107) SS BOND : bond 0.00607 ( 24) SS BOND : angle 2.76237 ( 48) hydrogen bonds : bond 0.03966 ( 1114) hydrogen bonds : angle 5.08813 ( 3198) link_ALPHA1-3 : bond 0.01486 ( 1) link_ALPHA1-3 : angle 2.94533 ( 3) link_BETA1-4 : bond 0.00467 ( 3) link_BETA1-4 : angle 1.54106 ( 9) link_NAG-ASN : bond 0.00219 ( 6) link_NAG-ASN : angle 1.87032 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 232 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 359 MET cc_start: 0.8103 (tpt) cc_final: 0.7579 (tpp) REVERT: B 420 TRP cc_start: 0.7788 (t60) cc_final: 0.7440 (t60) REVERT: D 921 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7616 (tp) REVERT: D 927 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8013 (mtpt) REVERT: D 1037 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6356 (m-80) REVERT: E 127 ILE cc_start: 0.7152 (OUTLIER) cc_final: 0.6901 (mp) REVERT: E 562 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8498 (t) REVERT: E 832 GLU cc_start: 0.7928 (mp0) cc_final: 0.7501 (mp0) REVERT: E 1043 ASP cc_start: 0.8399 (t70) cc_final: 0.7715 (t70) REVERT: E 1120 LEU cc_start: 0.2015 (OUTLIER) cc_final: 0.1585 (tp) REVERT: E 1281 MET cc_start: 0.6372 (ppp) cc_final: 0.5596 (ptt) REVERT: E 1342 HIS cc_start: 0.7283 (m170) cc_final: 0.6950 (m-70) REVERT: E 1373 ASN cc_start: 0.5908 (OUTLIER) cc_final: 0.5588 (p0) REVERT: E 1389 MET cc_start: 0.5753 (tpt) cc_final: 0.5299 (mpp) REVERT: E 1412 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: E 1597 ARG cc_start: 0.6299 (tpp-160) cc_final: 0.6022 (tpp-160) REVERT: E 1620 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6616 (t80) REVERT: E 1706 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7944 (t0) REVERT: E 1730 LEU cc_start: 0.5136 (OUTLIER) cc_final: 0.4856 (mm) REVERT: C 37 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: C 266 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7857 (mp0) outliers start: 106 outliers final: 62 residues processed: 322 average time/residue: 0.1868 time to fit residues: 97.5040 Evaluate side-chains 294 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 219 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 927 LYS Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1064 SER Chi-restraints excluded: chain D residue 1319 LEU Chi-restraints excluded: chain D residue 1365 VAL Chi-restraints excluded: chain D residue 1430 SER Chi-restraints excluded: chain D residue 1449 ASP Chi-restraints excluded: chain D residue 1494 HIS Chi-restraints excluded: chain D residue 1607 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain E residue 771 ASP Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain E residue 1027 TYR Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1142 THR Chi-restraints excluded: chain E residue 1210 ARG Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1304 ASP Chi-restraints excluded: chain E residue 1317 ILE Chi-restraints excluded: chain E residue 1373 ASN Chi-restraints excluded: chain E residue 1399 ILE Chi-restraints excluded: chain E residue 1412 GLU Chi-restraints excluded: chain E residue 1415 GLU Chi-restraints excluded: chain E residue 1504 LEU Chi-restraints excluded: chain E residue 1544 VAL Chi-restraints excluded: chain E residue 1546 VAL Chi-restraints excluded: chain E residue 1567 SER Chi-restraints excluded: chain E residue 1620 TYR Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1631 VAL Chi-restraints excluded: chain E residue 1706 ASN Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 333 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 638 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 276 optimal weight: 10.0000 chunk 151 optimal weight: 0.3980 chunk 290 optimal weight: 4.9990 chunk 292 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 329 optimal weight: 0.9980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN E 100 HIS ** E 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1342 HIS C 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101725 restraints weight = 62629.979| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.27 r_work: 0.3002 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 29627 Z= 0.213 Angle : 0.636 9.355 40185 Z= 0.327 Chirality : 0.046 0.196 4540 Planarity : 0.005 0.134 5190 Dihedral : 5.497 41.228 4182 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.37 % Rotamer: Outliers : 4.27 % Allowed : 23.91 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 3652 helix: 0.06 (0.20), residues: 689 sheet: 0.78 (0.14), residues: 1226 loop : -1.83 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 855 TYR 0.020 0.002 TYR E1027 PHE 0.024 0.002 PHE B 649 TRP 0.018 0.002 TRP B 420 HIS 0.006 0.001 HIS E 834 Details of bonding type rmsd covalent geometry : bond 0.00533 (29593) covalent geometry : angle 0.63016 (40107) SS BOND : bond 0.00411 ( 24) SS BOND : angle 1.99515 ( 48) hydrogen bonds : bond 0.04266 ( 1114) hydrogen bonds : angle 5.08194 ( 3198) link_ALPHA1-3 : bond 0.01387 ( 1) link_ALPHA1-3 : angle 3.05927 ( 3) link_BETA1-4 : bond 0.00360 ( 3) link_BETA1-4 : angle 1.68767 ( 9) link_NAG-ASN : bond 0.00237 ( 6) link_NAG-ASN : angle 2.02107 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 229 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 359 MET cc_start: 0.8095 (tpt) cc_final: 0.7758 (tpt) REVERT: B 420 TRP cc_start: 0.7896 (t60) cc_final: 0.7531 (t60) REVERT: B 443 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8688 (mmmt) REVERT: D 921 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7656 (tp) REVERT: D 1037 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.6275 (m-80) REVERT: D 1465 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: E 99 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7665 (mm) REVERT: E 127 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6660 (mp) REVERT: E 297 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8164 (mpt180) REVERT: E 484 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7798 (ttp80) REVERT: E 1043 ASP cc_start: 0.8425 (t70) cc_final: 0.7811 (t70) REVERT: E 1120 LEU cc_start: 0.2106 (OUTLIER) cc_final: 0.1702 (tp) REVERT: E 1342 HIS cc_start: 0.7081 (m90) cc_final: 0.6714 (m-70) REVERT: E 1373 ASN cc_start: 0.5930 (OUTLIER) cc_final: 0.5606 (p0) REVERT: E 1389 MET cc_start: 0.5801 (tpt) cc_final: 0.5474 (mpp) REVERT: E 1412 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: E 1597 ARG cc_start: 0.6443 (tpp-160) cc_final: 0.6167 (tpp-160) REVERT: E 1618 CYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6220 (m) REVERT: E 1620 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.6823 (t80) REVERT: E 1706 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7969 (t0) REVERT: E 1730 LEU cc_start: 0.5048 (OUTLIER) cc_final: 0.4756 (mm) REVERT: C 37 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7914 (pm20) REVERT: C 48 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7846 (m-30) REVERT: C 72 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: C 266 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7896 (mp0) outliers start: 136 outliers final: 85 residues processed: 346 average time/residue: 0.1864 time to fit residues: 104.1095 Evaluate side-chains 325 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 222 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 797 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1064 SER Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1300 LEU Chi-restraints excluded: chain D residue 1319 LEU Chi-restraints excluded: chain D residue 1365 VAL Chi-restraints excluded: chain D residue 1430 SER Chi-restraints excluded: chain D residue 1449 ASP Chi-restraints excluded: chain D residue 1465 GLN Chi-restraints excluded: chain D residue 1494 HIS Chi-restraints excluded: chain D residue 1588 ILE Chi-restraints excluded: chain D residue 1612 TRP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 297 ARG Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 484 ARG Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain E residue 771 ASP Chi-restraints excluded: chain E residue 781 ASN Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1027 TYR Chi-restraints excluded: chain E residue 1056 ILE Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1142 THR Chi-restraints excluded: chain E residue 1210 ARG Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1304 ASP Chi-restraints excluded: chain E residue 1317 ILE Chi-restraints excluded: chain E residue 1361 SER Chi-restraints excluded: chain E residue 1373 ASN Chi-restraints excluded: chain E residue 1399 ILE Chi-restraints excluded: chain E residue 1412 GLU Chi-restraints excluded: chain E residue 1415 GLU Chi-restraints excluded: chain E residue 1469 THR Chi-restraints excluded: chain E residue 1504 LEU Chi-restraints excluded: chain E residue 1544 VAL Chi-restraints excluded: chain E residue 1546 VAL Chi-restraints excluded: chain E residue 1548 LEU Chi-restraints excluded: chain E residue 1563 GLU Chi-restraints excluded: chain E residue 1567 SER Chi-restraints excluded: chain E residue 1618 CYS Chi-restraints excluded: chain E residue 1620 TYR Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1631 VAL Chi-restraints excluded: chain E residue 1657 VAL Chi-restraints excluded: chain E residue 1706 ASN Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 333 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 638 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 199 optimal weight: 0.5980 chunk 258 optimal weight: 30.0000 chunk 152 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 296 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1723 GLN C 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.153552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.102722 restraints weight = 62505.925| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.33 r_work: 0.3012 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 29627 Z= 0.150 Angle : 0.595 16.732 40185 Z= 0.306 Chirality : 0.045 0.233 4540 Planarity : 0.005 0.129 5190 Dihedral : 5.265 40.652 4180 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 4.39 % Allowed : 24.04 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 3652 helix: 0.22 (0.20), residues: 691 sheet: 0.87 (0.15), residues: 1194 loop : -1.75 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 855 TYR 0.018 0.001 TYR E1027 PHE 0.025 0.001 PHE B 649 TRP 0.023 0.001 TRP B 518 HIS 0.004 0.001 HIS E 834 Details of bonding type rmsd covalent geometry : bond 0.00370 (29593) covalent geometry : angle 0.59032 (40107) SS BOND : bond 0.00442 ( 24) SS BOND : angle 1.76453 ( 48) hydrogen bonds : bond 0.03759 ( 1114) hydrogen bonds : angle 4.92071 ( 3198) link_ALPHA1-3 : bond 0.01232 ( 1) link_ALPHA1-3 : angle 2.74550 ( 3) link_BETA1-4 : bond 0.00540 ( 3) link_BETA1-4 : angle 1.49432 ( 9) link_NAG-ASN : bond 0.00184 ( 6) link_NAG-ASN : angle 1.88092 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 226 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 359 MET cc_start: 0.8086 (tpt) cc_final: 0.7731 (tpt) REVERT: B 420 TRP cc_start: 0.7849 (t60) cc_final: 0.7483 (t60) REVERT: B 556 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: B 649 PHE cc_start: 0.6604 (m-10) cc_final: 0.6282 (m-10) REVERT: D 921 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7632 (tp) REVERT: D 1037 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: D 1522 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6169 (mtpp) REVERT: E 99 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7681 (mm) REVERT: E 127 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6738 (mp) REVERT: E 297 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8180 (mpt180) REVERT: E 484 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7785 (ttp80) REVERT: E 562 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8537 (t) REVERT: E 919 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.6350 (t80) REVERT: E 1043 ASP cc_start: 0.8436 (t70) cc_final: 0.8080 (t70) REVERT: E 1120 LEU cc_start: 0.2078 (OUTLIER) cc_final: 0.1686 (tp) REVERT: E 1218 MET cc_start: 0.5335 (ptp) cc_final: 0.5081 (ptt) REVERT: E 1342 HIS cc_start: 0.7279 (m90) cc_final: 0.6949 (m-70) REVERT: E 1389 MET cc_start: 0.5743 (tpt) cc_final: 0.5430 (mpp) REVERT: E 1412 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: E 1597 ARG cc_start: 0.6377 (tpp-160) cc_final: 0.6131 (tpp-160) REVERT: E 1613 ARG cc_start: 0.7214 (mtm180) cc_final: 0.6831 (mtm180) REVERT: E 1618 CYS cc_start: 0.6550 (OUTLIER) cc_final: 0.6175 (m) REVERT: E 1706 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7953 (t0) REVERT: E 1730 LEU cc_start: 0.5081 (OUTLIER) cc_final: 0.4780 (mm) REVERT: C 37 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: C 48 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: C 72 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: C 266 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7869 (mp0) outliers start: 140 outliers final: 88 residues processed: 347 average time/residue: 0.1831 time to fit residues: 102.4556 Evaluate side-chains 323 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 216 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1064 SER Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1300 LEU Chi-restraints excluded: chain D residue 1319 LEU Chi-restraints excluded: chain D residue 1324 THR Chi-restraints excluded: chain D residue 1365 VAL Chi-restraints excluded: chain D residue 1430 SER Chi-restraints excluded: chain D residue 1494 HIS Chi-restraints excluded: chain D residue 1522 LYS Chi-restraints excluded: chain D residue 1607 LEU Chi-restraints excluded: chain D residue 1612 TRP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 297 ARG Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 484 ARG Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain E residue 771 ASP Chi-restraints excluded: chain E residue 781 ASN Chi-restraints excluded: chain E residue 841 MET Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain E residue 919 PHE Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1027 TYR Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1142 THR Chi-restraints excluded: chain E residue 1210 ARG Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1269 LEU Chi-restraints excluded: chain E residue 1304 ASP Chi-restraints excluded: chain E residue 1317 ILE Chi-restraints excluded: chain E residue 1361 SER Chi-restraints excluded: chain E residue 1399 ILE Chi-restraints excluded: chain E residue 1410 THR Chi-restraints excluded: chain E residue 1412 GLU Chi-restraints excluded: chain E residue 1415 GLU Chi-restraints excluded: chain E residue 1504 LEU Chi-restraints excluded: chain E residue 1544 VAL Chi-restraints excluded: chain E residue 1546 VAL Chi-restraints excluded: chain E residue 1548 LEU Chi-restraints excluded: chain E residue 1563 GLU Chi-restraints excluded: chain E residue 1567 SER Chi-restraints excluded: chain E residue 1618 CYS Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1631 VAL Chi-restraints excluded: chain E residue 1648 THR Chi-restraints excluded: chain E residue 1657 VAL Chi-restraints excluded: chain E residue 1706 ASN Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 333 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 638 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 118 optimal weight: 8.9990 chunk 296 optimal weight: 6.9990 chunk 319 optimal weight: 0.2980 chunk 128 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 320 optimal weight: 0.8980 chunk 351 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 336 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1191 HIS E1414 ASN C 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.154618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103479 restraints weight = 59071.604| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.31 r_work: 0.3027 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 29627 Z= 0.145 Angle : 0.582 14.197 40185 Z= 0.300 Chirality : 0.044 0.277 4540 Planarity : 0.005 0.125 5190 Dihedral : 5.093 39.232 4180 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.05 % Favored : 95.92 % Rotamer: Outliers : 3.92 % Allowed : 24.44 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3652 helix: 0.25 (0.20), residues: 703 sheet: 0.92 (0.15), residues: 1192 loop : -1.66 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 666 TYR 0.016 0.001 TYR E1027 PHE 0.021 0.001 PHE B 649 TRP 0.022 0.001 TRP B 518 HIS 0.004 0.001 HIS E 834 Details of bonding type rmsd covalent geometry : bond 0.00362 (29593) covalent geometry : angle 0.57839 (40107) SS BOND : bond 0.00429 ( 24) SS BOND : angle 1.35132 ( 48) hydrogen bonds : bond 0.03581 ( 1114) hydrogen bonds : angle 4.79406 ( 3198) link_ALPHA1-3 : bond 0.01334 ( 1) link_ALPHA1-3 : angle 2.66398 ( 3) link_BETA1-4 : bond 0.00470 ( 3) link_BETA1-4 : angle 1.48504 ( 9) link_NAG-ASN : bond 0.00171 ( 6) link_NAG-ASN : angle 1.86712 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 230 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: B 359 MET cc_start: 0.8081 (tpt) cc_final: 0.7734 (tpt) REVERT: B 420 TRP cc_start: 0.7874 (t60) cc_final: 0.7496 (t60) REVERT: B 443 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8682 (mmmt) REVERT: D 1037 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6392 (m-80) REVERT: D 1465 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: D 1522 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6139 (mtpp) REVERT: D 1553 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6488 (mt0) REVERT: E 99 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7665 (mm) REVERT: E 127 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6681 (mp) REVERT: E 238 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8614 (mp) REVERT: E 297 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8165 (mpt180) REVERT: E 484 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7779 (ttp80) REVERT: E 562 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8528 (t) REVERT: E 919 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.6223 (t80) REVERT: E 1043 ASP cc_start: 0.8353 (t70) cc_final: 0.8032 (t70) REVERT: E 1120 LEU cc_start: 0.2092 (OUTLIER) cc_final: 0.1645 (tp) REVERT: E 1218 MET cc_start: 0.5331 (ptp) cc_final: 0.5069 (ptt) REVERT: E 1342 HIS cc_start: 0.7384 (m90) cc_final: 0.7033 (m-70) REVERT: E 1373 ASN cc_start: 0.6046 (OUTLIER) cc_final: 0.5711 (p0) REVERT: E 1389 MET cc_start: 0.5717 (tpt) cc_final: 0.5304 (mpp) REVERT: E 1412 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: E 1597 ARG cc_start: 0.6369 (tpp-160) cc_final: 0.6137 (tpp-160) REVERT: E 1613 ARG cc_start: 0.7170 (mtm180) cc_final: 0.6816 (mtm180) REVERT: E 1618 CYS cc_start: 0.6395 (OUTLIER) cc_final: 0.5994 (m) REVERT: E 1706 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8087 (t0) REVERT: E 1730 LEU cc_start: 0.5066 (OUTLIER) cc_final: 0.4760 (mm) REVERT: C 37 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: C 72 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: C 266 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7855 (mp0) outliers start: 125 outliers final: 89 residues processed: 338 average time/residue: 0.1835 time to fit residues: 99.4983 Evaluate side-chains 333 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 224 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 797 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1064 SER Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1300 LEU Chi-restraints excluded: chain D residue 1308 THR Chi-restraints excluded: chain D residue 1319 LEU Chi-restraints excluded: chain D residue 1324 THR Chi-restraints excluded: chain D residue 1365 VAL Chi-restraints excluded: chain D residue 1402 ILE Chi-restraints excluded: chain D residue 1430 SER Chi-restraints excluded: chain D residue 1465 GLN Chi-restraints excluded: chain D residue 1494 HIS Chi-restraints excluded: chain D residue 1522 LYS Chi-restraints excluded: chain D residue 1553 GLN Chi-restraints excluded: chain D residue 1607 LEU Chi-restraints excluded: chain D residue 1612 TRP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 297 ARG Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 484 ARG Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain E residue 771 ASP Chi-restraints excluded: chain E residue 781 ASN Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain E residue 919 PHE Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1027 TYR Chi-restraints excluded: chain E residue 1056 ILE Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1142 THR Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1269 LEU Chi-restraints excluded: chain E residue 1317 ILE Chi-restraints excluded: chain E residue 1347 ASN Chi-restraints excluded: chain E residue 1361 SER Chi-restraints excluded: chain E residue 1373 ASN Chi-restraints excluded: chain E residue 1399 ILE Chi-restraints excluded: chain E residue 1410 THR Chi-restraints excluded: chain E residue 1412 GLU Chi-restraints excluded: chain E residue 1415 GLU Chi-restraints excluded: chain E residue 1504 LEU Chi-restraints excluded: chain E residue 1544 VAL Chi-restraints excluded: chain E residue 1546 VAL Chi-restraints excluded: chain E residue 1548 LEU Chi-restraints excluded: chain E residue 1563 GLU Chi-restraints excluded: chain E residue 1618 CYS Chi-restraints excluded: chain E residue 1631 VAL Chi-restraints excluded: chain E residue 1648 THR Chi-restraints excluded: chain E residue 1657 VAL Chi-restraints excluded: chain E residue 1706 ASN Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 333 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 359 optimal weight: 0.9980 chunk 280 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 278 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.155209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103459 restraints weight = 47770.996| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.09 r_work: 0.3045 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 29627 Z= 0.128 Angle : 0.559 10.835 40185 Z= 0.287 Chirality : 0.044 0.333 4540 Planarity : 0.005 0.121 5190 Dihedral : 4.932 37.313 4180 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 3.67 % Allowed : 24.76 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3652 helix: 0.32 (0.20), residues: 710 sheet: 0.96 (0.15), residues: 1193 loop : -1.58 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1210 TYR 0.015 0.001 TYR C 446 PHE 0.020 0.001 PHE B 649 TRP 0.021 0.001 TRP B 518 HIS 0.008 0.001 HIS E1271 Details of bonding type rmsd covalent geometry : bond 0.00318 (29593) covalent geometry : angle 0.55587 (40107) SS BOND : bond 0.00332 ( 24) SS BOND : angle 1.11060 ( 48) hydrogen bonds : bond 0.03376 ( 1114) hydrogen bonds : angle 4.70418 ( 3198) link_ALPHA1-3 : bond 0.01156 ( 1) link_ALPHA1-3 : angle 2.37470 ( 3) link_BETA1-4 : bond 0.00468 ( 3) link_BETA1-4 : angle 1.44166 ( 9) link_NAG-ASN : bond 0.00188 ( 6) link_NAG-ASN : angle 1.77730 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 236 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: B 359 MET cc_start: 0.8053 (tpt) cc_final: 0.7707 (tpt) REVERT: B 420 TRP cc_start: 0.7890 (t60) cc_final: 0.7499 (t60) REVERT: B 443 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8679 (mmmt) REVERT: D 1037 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: D 1465 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: D 1522 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6124 (mtpp) REVERT: D 1553 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6544 (mt0) REVERT: E 99 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7705 (mm) REVERT: E 127 ILE cc_start: 0.6883 (OUTLIER) cc_final: 0.6569 (mp) REVERT: E 297 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8215 (mpt180) REVERT: E 484 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7773 (ttp80) REVERT: E 562 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8521 (t) REVERT: E 919 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.6301 (t80) REVERT: E 1043 ASP cc_start: 0.8267 (t70) cc_final: 0.7957 (t70) REVERT: E 1218 MET cc_start: 0.5328 (ptp) cc_final: 0.5049 (ptt) REVERT: E 1373 ASN cc_start: 0.6035 (OUTLIER) cc_final: 0.5700 (p0) REVERT: E 1389 MET cc_start: 0.5686 (tpt) cc_final: 0.5408 (mpp) REVERT: E 1412 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: E 1597 ARG cc_start: 0.6419 (tpp-160) cc_final: 0.6187 (tpp-160) REVERT: E 1618 CYS cc_start: 0.6502 (OUTLIER) cc_final: 0.6075 (m) REVERT: E 1706 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.8069 (t0) REVERT: E 1730 LEU cc_start: 0.5260 (OUTLIER) cc_final: 0.4975 (mm) REVERT: C 37 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: C 72 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: C 83 MET cc_start: 0.8947 (ttt) cc_final: 0.8297 (ttt) REVERT: C 266 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7775 (mp0) outliers start: 117 outliers final: 82 residues processed: 338 average time/residue: 0.1806 time to fit residues: 98.3181 Evaluate side-chains 321 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 221 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1064 SER Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1300 LEU Chi-restraints excluded: chain D residue 1308 THR Chi-restraints excluded: chain D residue 1324 THR Chi-restraints excluded: chain D residue 1365 VAL Chi-restraints excluded: chain D residue 1388 ILE Chi-restraints excluded: chain D residue 1402 ILE Chi-restraints excluded: chain D residue 1430 SER Chi-restraints excluded: chain D residue 1465 GLN Chi-restraints excluded: chain D residue 1494 HIS Chi-restraints excluded: chain D residue 1522 LYS Chi-restraints excluded: chain D residue 1553 GLN Chi-restraints excluded: chain D residue 1607 LEU Chi-restraints excluded: chain D residue 1612 TRP Chi-restraints excluded: chain D residue 1618 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 297 ARG Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 484 ARG Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain E residue 771 ASP Chi-restraints excluded: chain E residue 781 ASN Chi-restraints excluded: chain E residue 841 MET Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain E residue 919 PHE Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1027 TYR Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1142 THR Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1304 ASP Chi-restraints excluded: chain E residue 1317 ILE Chi-restraints excluded: chain E residue 1361 SER Chi-restraints excluded: chain E residue 1373 ASN Chi-restraints excluded: chain E residue 1399 ILE Chi-restraints excluded: chain E residue 1412 GLU Chi-restraints excluded: chain E residue 1415 GLU Chi-restraints excluded: chain E residue 1544 VAL Chi-restraints excluded: chain E residue 1546 VAL Chi-restraints excluded: chain E residue 1548 LEU Chi-restraints excluded: chain E residue 1563 GLU Chi-restraints excluded: chain E residue 1567 SER Chi-restraints excluded: chain E residue 1618 CYS Chi-restraints excluded: chain E residue 1631 VAL Chi-restraints excluded: chain E residue 1648 THR Chi-restraints excluded: chain E residue 1657 VAL Chi-restraints excluded: chain E residue 1706 ASN Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 333 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 260 optimal weight: 0.8980 chunk 336 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 190 optimal weight: 0.0000 chunk 7 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 chunk 360 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1271 HIS E1414 ASN C 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.153381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102810 restraints weight = 56325.314| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.11 r_work: 0.3034 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 29627 Z= 0.166 Angle : 0.590 10.542 40185 Z= 0.303 Chirality : 0.045 0.278 4540 Planarity : 0.005 0.119 5190 Dihedral : 4.986 38.068 4180 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 3.55 % Allowed : 25.04 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3652 helix: 0.28 (0.20), residues: 709 sheet: 0.93 (0.15), residues: 1211 loop : -1.58 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1507 TYR 0.017 0.001 TYR E1027 PHE 0.025 0.002 PHE B 649 TRP 0.020 0.001 TRP B 518 HIS 0.005 0.001 HIS E 834 Details of bonding type rmsd covalent geometry : bond 0.00418 (29593) covalent geometry : angle 0.58647 (40107) SS BOND : bond 0.00382 ( 24) SS BOND : angle 1.20540 ( 48) hydrogen bonds : bond 0.03681 ( 1114) hydrogen bonds : angle 4.75057 ( 3198) link_ALPHA1-3 : bond 0.01085 ( 1) link_ALPHA1-3 : angle 2.45873 ( 3) link_BETA1-4 : bond 0.00390 ( 3) link_BETA1-4 : angle 1.53944 ( 9) link_NAG-ASN : bond 0.00178 ( 6) link_NAG-ASN : angle 1.86702 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 227 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 359 MET cc_start: 0.8056 (tpt) cc_final: 0.7730 (tpt) REVERT: B 420 TRP cc_start: 0.7949 (t60) cc_final: 0.7519 (t60) REVERT: B 443 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8697 (mmmt) REVERT: D 1037 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6428 (m-80) REVERT: D 1465 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: D 1522 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6121 (mtpp) REVERT: D 1553 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6449 (mt0) REVERT: E 43 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8946 (tt) REVERT: E 99 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7682 (mm) REVERT: E 127 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6618 (mp) REVERT: E 297 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8184 (mpt180) REVERT: E 484 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7771 (ttp80) REVERT: E 919 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.6325 (t80) REVERT: E 1043 ASP cc_start: 0.8359 (t70) cc_final: 0.8069 (t70) REVERT: E 1218 MET cc_start: 0.5361 (ptp) cc_final: 0.5080 (ptt) REVERT: E 1373 ASN cc_start: 0.6053 (OUTLIER) cc_final: 0.5697 (p0) REVERT: E 1389 MET cc_start: 0.5655 (tpt) cc_final: 0.5283 (mpp) REVERT: E 1412 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: E 1597 ARG cc_start: 0.6325 (tpp-160) cc_final: 0.6101 (tpp-160) REVERT: E 1613 ARG cc_start: 0.7287 (mtm180) cc_final: 0.6754 (mpp80) REVERT: E 1706 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8161 (t0) REVERT: E 1730 LEU cc_start: 0.5070 (OUTLIER) cc_final: 0.4738 (mm) REVERT: C 37 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: C 72 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: C 266 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7792 (mp0) outliers start: 113 outliers final: 87 residues processed: 323 average time/residue: 0.1992 time to fit residues: 102.8584 Evaluate side-chains 329 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 225 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 797 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1064 SER Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1300 LEU Chi-restraints excluded: chain D residue 1308 THR Chi-restraints excluded: chain D residue 1324 THR Chi-restraints excluded: chain D residue 1365 VAL Chi-restraints excluded: chain D residue 1388 ILE Chi-restraints excluded: chain D residue 1402 ILE Chi-restraints excluded: chain D residue 1465 GLN Chi-restraints excluded: chain D residue 1494 HIS Chi-restraints excluded: chain D residue 1522 LYS Chi-restraints excluded: chain D residue 1553 GLN Chi-restraints excluded: chain D residue 1607 LEU Chi-restraints excluded: chain D residue 1612 TRP Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 297 ARG Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 484 ARG Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain E residue 771 ASP Chi-restraints excluded: chain E residue 781 ASN Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain E residue 919 PHE Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1056 ILE Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1142 THR Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1269 LEU Chi-restraints excluded: chain E residue 1317 ILE Chi-restraints excluded: chain E residue 1347 ASN Chi-restraints excluded: chain E residue 1361 SER Chi-restraints excluded: chain E residue 1373 ASN Chi-restraints excluded: chain E residue 1399 ILE Chi-restraints excluded: chain E residue 1410 THR Chi-restraints excluded: chain E residue 1412 GLU Chi-restraints excluded: chain E residue 1415 GLU Chi-restraints excluded: chain E residue 1544 VAL Chi-restraints excluded: chain E residue 1546 VAL Chi-restraints excluded: chain E residue 1548 LEU Chi-restraints excluded: chain E residue 1563 GLU Chi-restraints excluded: chain E residue 1567 SER Chi-restraints excluded: chain E residue 1618 CYS Chi-restraints excluded: chain E residue 1631 VAL Chi-restraints excluded: chain E residue 1648 THR Chi-restraints excluded: chain E residue 1657 VAL Chi-restraints excluded: chain E residue 1706 ASN Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 333 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 79 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 242 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 348 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 350 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.153575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102215 restraints weight = 68263.896| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.52 r_work: 0.3006 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 29627 Z= 0.178 Angle : 0.601 10.395 40185 Z= 0.308 Chirality : 0.045 0.296 4540 Planarity : 0.005 0.117 5190 Dihedral : 5.046 38.834 4180 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.11 % Favored : 95.87 % Rotamer: Outliers : 3.33 % Allowed : 25.45 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3652 helix: 0.24 (0.20), residues: 716 sheet: 0.89 (0.15), residues: 1213 loop : -1.56 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1676 TYR 0.019 0.001 TYR E1027 PHE 0.035 0.002 PHE E 974 TRP 0.024 0.001 TRP B 518 HIS 0.005 0.001 HIS E 834 Details of bonding type rmsd covalent geometry : bond 0.00449 (29593) covalent geometry : angle 0.59744 (40107) SS BOND : bond 0.00367 ( 24) SS BOND : angle 1.22456 ( 48) hydrogen bonds : bond 0.03799 ( 1114) hydrogen bonds : angle 4.78875 ( 3198) link_ALPHA1-3 : bond 0.01051 ( 1) link_ALPHA1-3 : angle 2.36433 ( 3) link_BETA1-4 : bond 0.00443 ( 3) link_BETA1-4 : angle 1.59713 ( 9) link_NAG-ASN : bond 0.00185 ( 6) link_NAG-ASN : angle 1.91152 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 225 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: B 359 MET cc_start: 0.8012 (tpt) cc_final: 0.7666 (tpt) REVERT: B 420 TRP cc_start: 0.8021 (t60) cc_final: 0.7562 (t60) REVERT: B 443 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8710 (mmmt) REVERT: D 973 ASP cc_start: 0.7422 (t0) cc_final: 0.7118 (t0) REVERT: D 1037 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6495 (m-80) REVERT: D 1465 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: D 1522 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6186 (mtpp) REVERT: D 1595 LYS cc_start: 0.7927 (mmtt) cc_final: 0.7471 (mttp) REVERT: E 99 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7673 (mm) REVERT: E 127 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6518 (mp) REVERT: E 297 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8210 (mmt-90) REVERT: E 484 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7826 (ttp80) REVERT: E 919 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.6307 (t80) REVERT: E 1043 ASP cc_start: 0.8425 (t70) cc_final: 0.8159 (t70) REVERT: E 1218 MET cc_start: 0.5349 (ptp) cc_final: 0.5033 (ptt) REVERT: E 1373 ASN cc_start: 0.5964 (OUTLIER) cc_final: 0.5602 (p0) REVERT: E 1389 MET cc_start: 0.5675 (tpt) cc_final: 0.5153 (mpp) REVERT: E 1412 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: E 1597 ARG cc_start: 0.6362 (tpp-160) cc_final: 0.6148 (tpp-160) REVERT: E 1618 CYS cc_start: 0.6547 (OUTLIER) cc_final: 0.6130 (m) REVERT: E 1706 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8149 (t0) REVERT: E 1730 LEU cc_start: 0.5105 (OUTLIER) cc_final: 0.4767 (mm) REVERT: C 37 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: C 72 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: C 266 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7818 (mp0) outliers start: 106 outliers final: 86 residues processed: 316 average time/residue: 0.1984 time to fit residues: 100.4084 Evaluate side-chains 325 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 223 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 756 ILE Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 797 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1064 SER Chi-restraints excluded: chain D residue 1269 THR Chi-restraints excluded: chain D residue 1300 LEU Chi-restraints excluded: chain D residue 1308 THR Chi-restraints excluded: chain D residue 1324 THR Chi-restraints excluded: chain D residue 1365 VAL Chi-restraints excluded: chain D residue 1402 ILE Chi-restraints excluded: chain D residue 1430 SER Chi-restraints excluded: chain D residue 1465 GLN Chi-restraints excluded: chain D residue 1494 HIS Chi-restraints excluded: chain D residue 1522 LYS Chi-restraints excluded: chain D residue 1607 LEU Chi-restraints excluded: chain D residue 1612 TRP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 297 ARG Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 484 ARG Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 562 VAL Chi-restraints excluded: chain E residue 771 ASP Chi-restraints excluded: chain E residue 781 ASN Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain E residue 919 PHE Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 1027 TYR Chi-restraints excluded: chain E residue 1056 ILE Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1142 THR Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1317 ILE Chi-restraints excluded: chain E residue 1347 ASN Chi-restraints excluded: chain E residue 1361 SER Chi-restraints excluded: chain E residue 1373 ASN Chi-restraints excluded: chain E residue 1399 ILE Chi-restraints excluded: chain E residue 1410 THR Chi-restraints excluded: chain E residue 1412 GLU Chi-restraints excluded: chain E residue 1415 GLU Chi-restraints excluded: chain E residue 1544 VAL Chi-restraints excluded: chain E residue 1546 VAL Chi-restraints excluded: chain E residue 1548 LEU Chi-restraints excluded: chain E residue 1563 GLU Chi-restraints excluded: chain E residue 1567 SER Chi-restraints excluded: chain E residue 1618 CYS Chi-restraints excluded: chain E residue 1631 VAL Chi-restraints excluded: chain E residue 1648 THR Chi-restraints excluded: chain E residue 1657 VAL Chi-restraints excluded: chain E residue 1706 ASN Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 333 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 142 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 333 optimal weight: 0.8980 chunk 355 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 chunk 348 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 12 optimal weight: 0.0980 chunk 288 optimal weight: 1.9990 chunk 360 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN D1127 GLN ** D1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1601 HIS ** E 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.154777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104365 restraints weight = 58346.253| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.25 r_work: 0.3059 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 29627 Z= 0.123 Angle : 0.561 11.165 40185 Z= 0.289 Chirality : 0.044 0.286 4540 Planarity : 0.005 0.115 5190 Dihedral : 4.845 36.758 4180 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 3.23 % Allowed : 25.57 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3652 helix: 0.40 (0.20), residues: 715 sheet: 1.01 (0.15), residues: 1183 loop : -1.49 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1676 TYR 0.015 0.001 TYR C 446 PHE 0.038 0.001 PHE E 974 TRP 0.021 0.001 TRP B 518 HIS 0.004 0.001 HIS B 507 Details of bonding type rmsd covalent geometry : bond 0.00307 (29593) covalent geometry : angle 0.55890 (40107) SS BOND : bond 0.00337 ( 24) SS BOND : angle 1.00305 ( 48) hydrogen bonds : bond 0.03294 ( 1114) hydrogen bonds : angle 4.63853 ( 3198) link_ALPHA1-3 : bond 0.01089 ( 1) link_ALPHA1-3 : angle 2.00453 ( 3) link_BETA1-4 : bond 0.00517 ( 3) link_BETA1-4 : angle 1.44424 ( 9) link_NAG-ASN : bond 0.00175 ( 6) link_NAG-ASN : angle 1.78021 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8251.22 seconds wall clock time: 141 minutes 36.53 seconds (8496.53 seconds total)