Starting phenix.real_space_refine on Wed Jun 18 22:13:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fhs_29102/06_2025/8fhs_29102.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fhs_29102/06_2025/8fhs_29102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fhs_29102/06_2025/8fhs_29102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fhs_29102/06_2025/8fhs_29102.map" model { file = "/net/cci-nas-00/data/ceres_data/8fhs_29102/06_2025/8fhs_29102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fhs_29102/06_2025/8fhs_29102.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians I 2 10.91 5 Ca 2 9.91 5 P 3 5.49 5 S 107 5.16 5 C 13559 2.51 5 N 3457 2.21 5 O 3844 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20975 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 10356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1282, 10356 Classifications: {'peptide': 1282} Link IDs: {'PTRANS': 40, 'TRANS': 1241} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 263 Unusual residues: {' CA': 1, '3PE': 2, 'BBI': 1, 'CLR': 4, 'WG6': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.51, per 1000 atoms: 0.55 Number of scatterers: 20975 At special positions: 0 Unit cell: (169.328, 173.784, 184.924, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) I 2 52.95 Ca 2 19.99 S 107 16.00 P 3 15.00 F 1 9.00 O 3844 8.00 N 3457 7.00 C 13559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1479 " - pdb=" SG CYS A1495 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.04 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 1 " - " ASN D 184 " " NAG D1202 " - " ASN D 92 " " NAG D1203 " - " ASN D 781 " " NAG E 1 " - " ASN D 348 " " NAG F 1 " - " ASN D 468 " " NAG G 1 " - " ASN D 613 " " NAG H 1 " - " ASN D 895 " Time building additional restraints: 5.33 Conformation dependent library (CDL) restraints added in 2.3 seconds 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4840 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 15 sheets defined 55.0% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.589A pdb=" N ALA A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 144 Processing helix chain 'A' and resid 153 through 181 removed outlier: 3.515A pdb=" N SER A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 217 removed outlier: 3.835A pdb=" N LEU A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 199 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.583A pdb=" N PHE A 239 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 241 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.597A pdb=" N ARG A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 247 " --> pdb=" O ARG A 243 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.761A pdb=" N VAL A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 268 through 290 Processing helix chain 'A' and resid 348 through 361 Processing helix chain 'A' and resid 364 through 376 removed outlier: 3.797A pdb=" N VAL A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 393 removed outlier: 3.782A pdb=" N PHE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 419 removed outlier: 3.718A pdb=" N LYS A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA A 417 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 446 removed outlier: 3.750A pdb=" N LYS A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU A 432 " --> pdb=" O GLN A 428 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 removed outlier: 3.605A pdb=" N LYS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 542 Processing helix chain 'A' and resid 549 through 579 Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 588 through 608 removed outlier: 3.570A pdb=" N CYS A 593 " --> pdb=" O ASN A 589 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 601 " --> pdb=" O CYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 630 removed outlier: 3.717A pdb=" N ARG A 620 " --> pdb=" O SER A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 647 removed outlier: 3.837A pdb=" N LEU A 637 " --> pdb=" O TYR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 673 Processing helix chain 'A' and resid 691 through 704 Processing helix chain 'A' and resid 707 through 719 removed outlier: 3.652A pdb=" N VAL A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.921A pdb=" N LEU A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 782 removed outlier: 4.106A pdb=" N PHE A 733 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 737 " --> pdb=" O PHE A 733 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA A 750 " --> pdb=" O ASN A 746 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 759 " --> pdb=" O ASN A 755 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU A 768 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU A 769 " --> pdb=" O ALA A 765 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 771 " --> pdb=" O LYS A 767 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 919 removed outlier: 3.649A pdb=" N ILE A 906 " --> pdb=" O PHE A 902 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 973 removed outlier: 4.956A pdb=" N TYR A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 973 " --> pdb=" O ILE A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.662A pdb=" N ASP A 993 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 994 " --> pdb=" O ASN A 990 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A1001 " --> pdb=" O VAL A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1004 No H-bonds generated for 'chain 'A' and resid 1002 through 1004' Processing helix chain 'A' and resid 1012 through 1018 removed outlier: 3.577A pdb=" N ILE A1016 " --> pdb=" O ASN A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1029 removed outlier: 3.621A pdb=" N VAL A1022 " --> pdb=" O VAL A1019 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A1023 " --> pdb=" O LEU A1020 " (cutoff:3.500A) Proline residue: A1025 - end of helix removed outlier: 3.820A pdb=" N ILE A1029 " --> pdb=" O LEU A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1071 removed outlier: 4.886A pdb=" N ASN A1051 " --> pdb=" O ARG A1047 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE A1052 " --> pdb=" O THR A1048 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A1055 " --> pdb=" O ASN A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1120 through 1133 Processing helix chain 'A' and resid 1136 through 1146 removed outlier: 3.804A pdb=" N ASP A1146 " --> pdb=" O TYR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1161 No H-bonds generated for 'chain 'A' and resid 1159 through 1161' Processing helix chain 'A' and resid 1162 through 1173 removed outlier: 3.930A pdb=" N PHE A1166 " --> pdb=" O ILE A1162 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A1170 " --> pdb=" O PHE A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1195 Processing helix chain 'A' and resid 1205 through 1215 Processing helix chain 'A' and resid 1226 through 1238 removed outlier: 3.532A pdb=" N SER A1238 " --> pdb=" O TYR A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1257 Processing helix chain 'A' and resid 1264 through 1294 Processing helix chain 'A' and resid 1294 through 1299 removed outlier: 4.046A pdb=" N PHE A1299 " --> pdb=" O PRO A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1322 removed outlier: 3.611A pdb=" N ILE A1316 " --> pdb=" O ILE A1312 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP A1317 " --> pdb=" O GLY A1313 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A1322 " --> pdb=" O VAL A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1383 removed outlier: 3.965A pdb=" N ARG A1380 " --> pdb=" O PHE A1376 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A1381 " --> pdb=" O ARG A1377 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A1383 " --> pdb=" O PHE A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1389 Processing helix chain 'A' and resid 1391 through 1408 Processing helix chain 'A' and resid 1408 through 1431 removed outlier: 4.297A pdb=" N ALA A1412 " --> pdb=" O LEU A1408 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A1415 " --> pdb=" O VAL A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1463 Processing helix chain 'A' and resid 1465 through 1473 removed outlier: 3.824A pdb=" N LEU A1471 " --> pdb=" O GLN A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1499 through 1525 removed outlier: 3.546A pdb=" N ALA A1512 " --> pdb=" O TYR A1508 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A1513 " --> pdb=" O MET A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1531 Processing helix chain 'A' and resid 1538 through 1550 removed outlier: 3.962A pdb=" N GLU A1544 " --> pdb=" O HIS A1540 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE A1545 " --> pdb=" O HIS A1541 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS A1546 " --> pdb=" O LEU A1542 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A1547 " --> pdb=" O ASP A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1564 through 1572 removed outlier: 3.737A pdb=" N ARG A1570 " --> pdb=" O VAL A1566 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A1572 " --> pdb=" O LEU A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1594 Processing helix chain 'A' and resid 1605 through 1618 Processing helix chain 'A' and resid 1625 through 1636 removed outlier: 3.951A pdb=" N ARG A1634 " --> pdb=" O ASN A1630 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1636 " --> pdb=" O GLU A1632 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 53 removed outlier: 3.887A pdb=" N SER D 35 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.656A pdb=" N VAL D 58 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP D 59 " --> pdb=" O ASN D 55 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 110 removed outlier: 3.516A pdb=" N ARG D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 188 through 200 removed outlier: 4.222A pdb=" N VAL D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.850A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 removed outlier: 3.531A pdb=" N VAL D 264 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 281 removed outlier: 3.804A pdb=" N LYS D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 369 through 376 Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.680A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'D' and resid 418 through 424 removed outlier: 3.514A pdb=" N ASN D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 431 removed outlier: 4.268A pdb=" N VAL D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 437 Processing helix chain 'D' and resid 438 through 442 Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.558A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 565 removed outlier: 3.710A pdb=" N GLU D 565 " --> pdb=" O PHE D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 removed outlier: 3.944A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP D 580 " --> pdb=" O ASN D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 646 removed outlier: 3.962A pdb=" N GLN D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 643 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER D 645 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU D 646 " --> pdb=" O ALA D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 651 Proline residue: D 650 - end of helix No H-bonds generated for 'chain 'D' and resid 647 through 651' Processing helix chain 'D' and resid 652 through 657 removed outlier: 3.501A pdb=" N SER D 656 " --> pdb=" O ASN D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 690 removed outlier: 3.723A pdb=" N ASP D 688 " --> pdb=" O ASN D 684 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 689 " --> pdb=" O GLU D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 718 removed outlier: 3.747A pdb=" N ILE D 702 " --> pdb=" O ASN D 698 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 709 " --> pdb=" O VAL D 705 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 715 " --> pdb=" O PHE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 750 removed outlier: 4.066A pdb=" N GLU D 750 " --> pdb=" O LYS D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.687A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN D 770 " --> pdb=" O ARG D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 removed outlier: 3.699A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN D 824 " --> pdb=" O SER D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 878 Processing helix chain 'D' and resid 879 through 889 Processing helix chain 'D' and resid 1021 through 1024 removed outlier: 3.610A pdb=" N CYS D1024 " --> pdb=" O LYS D1021 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1021 through 1024' Processing helix chain 'D' and resid 1042 through 1047 Processing helix chain 'D' and resid 1071 through 1076 removed outlier: 4.226A pdb=" N SER D1075 " --> pdb=" O CYS D1071 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY D1076 " --> pdb=" O GLY D1072 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1071 through 1076' Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.731A pdb=" N GLU C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 134 removed outlier: 3.731A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 190 through 208 removed outlier: 3.506A pdb=" N LEU C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 263 removed outlier: 3.746A pdb=" N GLN C 251 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 255 " --> pdb=" O GLN C 251 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 4.100A pdb=" N LYS C 282 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 removed outlier: 4.211A pdb=" N LEU C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN C 301 " --> pdb=" O PRO C 297 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 302 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 306 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 313 removed outlier: 4.047A pdb=" N MET C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 308 through 313' Processing helix chain 'C' and resid 316 through 327 removed outlier: 3.889A pdb=" N MET C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 327 " --> pdb=" O ASP C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 Processing helix chain 'C' and resid 341 through 360 removed outlier: 3.692A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 299 removed outlier: 3.554A pdb=" N THR A 297 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 331 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1077 through 1078 Processing sheet with id=AA3, first strand: chain 'A' and resid 1092 through 1096 Processing sheet with id=AA4, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AA5, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.715A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.715A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 464 " --> pdb=" O MET D 488 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AA8, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.303A pdb=" N ILE D 256 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE D 294 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL D 258 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE D 358 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE D 387 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL D 389 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR D 362 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL D 384 " --> pdb=" O TYR D 409 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR D 411 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE D 413 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER D 388 " --> pdb=" O ILE D 413 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 521 through 523 removed outlier: 6.213A pdb=" N ALA D 514 " --> pdb=" O LEU D 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 658 through 659 removed outlier: 3.676A pdb=" N ALA D 731 " --> pdb=" O LYS D 815 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 800 through 801 Processing sheet with id=AB3, first strand: chain 'D' and resid 859 through 861 removed outlier: 7.080A pdb=" N LEU D 859 " --> pdb=" O ASP D 854 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASP D 854 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET D 861 " --> pdb=" O ILE D 852 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D1018 " --> pdb=" O ASP D 849 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 851 " --> pdb=" O ILE D1016 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU D1019 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 892 through 904 removed outlier: 3.606A pdb=" N GLN D 980 " --> pdb=" O ASN D 895 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN D 901 " --> pdb=" O CYS D 974 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N CYS D 974 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL D 903 " --> pdb=" O GLN D 972 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN D 972 " --> pdb=" O VAL D 903 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 116 through 119 removed outlier: 4.326A pdb=" N ALA C 63 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 174 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP C 172 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 212 through 215 removed outlier: 6.282A pdb=" N VAL C 180 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 183 " --> pdb=" O VAL C 290 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2775 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: 7.44 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 6643 1.34 - 1.51: 5859 1.51 - 1.67: 8757 1.67 - 1.83: 166 1.83 - 1.99: 2 Bond restraints: 21427 Sorted by residual: bond pdb=" C17 WG6 A2303 " pdb=" O18 WG6 A2303 " ideal model delta sigma weight residual 1.406 1.673 -0.267 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C16 WG6 A2303 " pdb=" C17 WG6 A2303 " ideal model delta sigma weight residual 1.541 1.284 0.257 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C20 WG6 A2303 " pdb=" C21 WG6 A2303 " ideal model delta sigma weight residual 1.345 1.501 -0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C14 WG6 A2303 " pdb=" O18 WG6 A2303 " ideal model delta sigma weight residual 1.438 1.299 0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C25 WG6 A2303 " pdb=" N24 WG6 A2303 " ideal model delta sigma weight residual 1.374 1.490 -0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 21422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 28776 2.65 - 5.31: 210 5.31 - 7.96: 36 7.96 - 10.61: 9 10.61 - 13.27: 3 Bond angle restraints: 29034 Sorted by residual: angle pdb=" N VAL D 891 " pdb=" CA VAL D 891 " pdb=" C VAL D 891 " ideal model delta sigma weight residual 112.96 108.22 4.74 1.00e+00 1.00e+00 2.24e+01 angle pdb=" CAM BBI A2302 " pdb=" CAN BBI A2302 " pdb=" CAP BBI A2302 " ideal model delta sigma weight residual 118.51 131.78 -13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" CA PRO A1025 " pdb=" N PRO A1025 " pdb=" CD PRO A1025 " ideal model delta sigma weight residual 112.00 106.41 5.59 1.40e+00 5.10e-01 1.60e+01 angle pdb=" CAC BBI A2302 " pdb=" CAD BBI A2302 " pdb=" CAE BBI A2302 " ideal model delta sigma weight residual 112.57 124.38 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CB PRO A1025 " pdb=" CG PRO A1025 " pdb=" CD PRO A1025 " ideal model delta sigma weight residual 106.10 94.03 12.07 3.20e+00 9.77e-02 1.42e+01 ... (remaining 29029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.12: 12629 32.12 - 64.24: 582 64.24 - 96.36: 66 96.36 - 128.48: 17 128.48 - 160.60: 3 Dihedral angle restraints: 13297 sinusoidal: 5822 harmonic: 7475 Sorted by residual: dihedral pdb=" CB CYS A 316 " pdb=" SG CYS A 316 " pdb=" SG CYS A 332 " pdb=" CB CYS A 332 " ideal model delta sinusoidal sigma weight residual -86.00 -165.69 79.69 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS D 404 " pdb=" SG CYS D 404 " pdb=" SG CYS D1071 " pdb=" CB CYS D1071 " ideal model delta sinusoidal sigma weight residual 93.00 135.59 -42.59 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CB CYS A1479 " pdb=" SG CYS A1479 " pdb=" SG CYS A1495 " pdb=" CB CYS A1495 " ideal model delta sinusoidal sigma weight residual 93.00 131.69 -38.69 1 1.00e+01 1.00e-02 2.11e+01 ... (remaining 13294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3187 0.094 - 0.187: 122 0.187 - 0.281: 4 0.281 - 0.375: 3 0.375 - 0.468: 1 Chirality restraints: 3317 Sorted by residual: chirality pdb=" P10 WG6 A2303 " pdb=" O11 WG6 A2303 " pdb=" O12 WG6 A2303 " pdb=" O30 WG6 A2303 " both_signs ideal model delta sigma weight residual True 2.67 -3.14 -0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 184 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C1 NAG D1202 " pdb=" ND2 ASN D 92 " pdb=" C2 NAG D1202 " pdb=" O5 NAG D1202 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 3314 not shown) Planarity restraints: 3644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 140 " 0.034 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO C 141 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 141 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 141 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D1068 " -0.010 2.00e-02 2.50e+03 1.20e-02 2.86e+00 pdb=" CG TYR D1068 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR D1068 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D1068 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR D1068 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D1068 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR D1068 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D1068 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 27 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO D 28 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 28 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 28 " -0.022 5.00e-02 4.00e+02 ... (remaining 3641 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.75: 2927 2.75 - 3.31: 21675 3.31 - 3.86: 34816 3.86 - 4.41: 42656 4.41 - 4.96: 71478 Nonbonded interactions: 173552 Sorted by model distance: nonbonded pdb=" OD1 ASN D 675 " pdb=" OG1 THR D 677 " model vdw 2.203 3.040 nonbonded pdb=" OG SER D 594 " pdb=" O ASP D 596 " model vdw 2.209 3.040 nonbonded pdb=" OG SER C 100 " pdb=" OD1 ASP C 102 " model vdw 2.214 3.040 nonbonded pdb=" O TYR D 61 " pdb=" OH TYR D 68 " model vdw 2.229 3.040 nonbonded pdb=" N GLU D 678 " pdb=" OE1 GLU D 678 " model vdw 2.230 3.120 ... (remaining 173547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 45.880 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 0.267 21452 Z= 0.243 Angle : 0.632 13.268 29099 Z= 0.303 Chirality : 0.043 0.468 3317 Planarity : 0.003 0.051 3637 Dihedral : 17.882 160.600 8427 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 0.71 % Allowed : 13.97 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2524 helix: 0.21 (0.16), residues: 1139 sheet: -0.59 (0.34), residues: 259 loop : -1.31 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1233 HIS 0.003 0.001 HIS D 306 PHE 0.018 0.001 PHE D 990 TYR 0.030 0.001 TYR D1068 ARG 0.006 0.000 ARG A 418 Details of bonding type rmsd link_NAG-ASN : bond 0.01159 ( 7) link_NAG-ASN : angle 5.64225 ( 21) link_BETA1-4 : bond 0.00767 ( 8) link_BETA1-4 : angle 2.77975 ( 24) hydrogen bonds : bond 0.23082 ( 966) hydrogen bonds : angle 7.31195 ( 2775) SS BOND : bond 0.00198 ( 10) SS BOND : angle 1.01839 ( 20) covalent geometry : bond 0.00491 (21427) covalent geometry : angle 0.60861 (29034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 2.345 Fit side-chains REVERT: A 554 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 1474 MET cc_start: 0.8359 (mmt) cc_final: 0.7947 (mmt) REVERT: D 772 ASN cc_start: 0.8169 (m-40) cc_final: 0.7741 (p0) REVERT: D 861 MET cc_start: 0.7575 (tpp) cc_final: 0.7333 (mmt) outliers start: 16 outliers final: 4 residues processed: 286 average time/residue: 0.3171 time to fit residues: 144.2649 Evaluate side-chains 264 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 260 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 1062 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 102 optimal weight: 0.0970 chunk 199 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 230 optimal weight: 10.0000 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1607 ASN D 181 ASN C 348 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.180405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136496 restraints weight = 25195.232| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.02 r_work: 0.3190 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21452 Z= 0.149 Angle : 0.610 11.700 29099 Z= 0.303 Chirality : 0.044 0.292 3317 Planarity : 0.004 0.049 3637 Dihedral : 12.394 151.625 3486 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 1.86 % Allowed : 14.63 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2524 helix: 0.69 (0.15), residues: 1195 sheet: -0.60 (0.32), residues: 271 loop : -1.43 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1233 HIS 0.007 0.001 HIS D1004 PHE 0.021 0.001 PHE D 990 TYR 0.014 0.001 TYR D1068 ARG 0.004 0.000 ARG A 775 Details of bonding type rmsd link_NAG-ASN : bond 0.01194 ( 7) link_NAG-ASN : angle 5.73883 ( 21) link_BETA1-4 : bond 0.00727 ( 8) link_BETA1-4 : angle 2.60261 ( 24) hydrogen bonds : bond 0.04930 ( 966) hydrogen bonds : angle 4.76391 ( 2775) SS BOND : bond 0.00171 ( 10) SS BOND : angle 1.10509 ( 20) covalent geometry : bond 0.00342 (21427) covalent geometry : angle 0.58528 (29034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 2.383 Fit side-chains REVERT: A 213 GLU cc_start: 0.7878 (tp30) cc_final: 0.7580 (tp30) REVERT: A 1062 MET cc_start: 0.8715 (mtp) cc_final: 0.8462 (mtt) REVERT: A 1245 MET cc_start: 0.8327 (mmm) cc_final: 0.7949 (mmm) REVERT: A 1399 TRP cc_start: 0.8651 (t-100) cc_final: 0.8438 (t-100) REVERT: A 1474 MET cc_start: 0.8464 (mmt) cc_final: 0.8056 (mmt) REVERT: A 1605 MET cc_start: 0.6632 (tmm) cc_final: 0.6099 (tmm) REVERT: D 43 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7375 (p0) REVERT: D 772 ASN cc_start: 0.8386 (m-40) cc_final: 0.7808 (p0) REVERT: D 871 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.6818 (mt) REVERT: C 58 LYS cc_start: 0.3382 (tppp) cc_final: 0.2816 (tptt) outliers start: 42 outliers final: 23 residues processed: 310 average time/residue: 0.3039 time to fit residues: 152.9533 Evaluate side-chains 291 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 266 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1427 MET Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 335 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 124 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 159 optimal weight: 0.0970 chunk 30 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 ASN A1607 ASN D1062 ASN C 348 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.177922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130922 restraints weight = 24524.362| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.10 r_work: 0.3069 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21452 Z= 0.173 Angle : 0.608 12.540 29099 Z= 0.298 Chirality : 0.044 0.268 3317 Planarity : 0.004 0.047 3637 Dihedral : 11.308 148.046 3477 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.78 % Favored : 94.18 % Rotamer: Outliers : 2.52 % Allowed : 15.38 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2524 helix: 0.77 (0.15), residues: 1204 sheet: -0.67 (0.31), residues: 272 loop : -1.45 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1233 HIS 0.005 0.001 HIS C 94 PHE 0.019 0.001 PHE A1401 TYR 0.013 0.001 TYR D 764 ARG 0.003 0.000 ARG A1443 Details of bonding type rmsd link_NAG-ASN : bond 0.00997 ( 7) link_NAG-ASN : angle 5.19988 ( 21) link_BETA1-4 : bond 0.00718 ( 8) link_BETA1-4 : angle 2.87385 ( 24) hydrogen bonds : bond 0.04507 ( 966) hydrogen bonds : angle 4.46388 ( 2775) SS BOND : bond 0.00170 ( 10) SS BOND : angle 1.32449 ( 20) covalent geometry : bond 0.00414 (21427) covalent geometry : angle 0.58506 (29034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 ILE cc_start: 0.8340 (pt) cc_final: 0.8072 (pt) REVERT: A 213 GLU cc_start: 0.7887 (tp30) cc_final: 0.7554 (tp30) REVERT: A 554 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8300 (mm-30) REVERT: A 571 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6864 (ttp) REVERT: A 587 LEU cc_start: 0.8358 (tp) cc_final: 0.8076 (tt) REVERT: A 1062 MET cc_start: 0.8511 (mtp) cc_final: 0.8228 (mtt) REVERT: A 1164 ILE cc_start: 0.8685 (pt) cc_final: 0.8438 (mm) REVERT: A 1383 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7811 (mtm110) REVERT: A 1474 MET cc_start: 0.8486 (mmt) cc_final: 0.8042 (mmt) REVERT: D 43 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7222 (p0) REVERT: D 309 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: D 772 ASN cc_start: 0.8258 (m-40) cc_final: 0.7677 (p0) REVERT: C 58 LYS cc_start: 0.3397 (tppp) cc_final: 0.2912 (tptt) outliers start: 57 outliers final: 32 residues processed: 316 average time/residue: 0.3142 time to fit residues: 160.4848 Evaluate side-chains 295 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1383 ARG Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 1062 ASN Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 159 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 175 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.181048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137817 restraints weight = 25649.588| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.03 r_work: 0.3204 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21452 Z= 0.111 Angle : 0.559 10.625 29099 Z= 0.273 Chirality : 0.042 0.285 3317 Planarity : 0.003 0.048 3637 Dihedral : 10.707 144.018 3477 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.47 % Favored : 94.49 % Rotamer: Outliers : 2.08 % Allowed : 17.37 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2524 helix: 0.96 (0.15), residues: 1206 sheet: -0.60 (0.31), residues: 271 loop : -1.41 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1233 HIS 0.004 0.001 HIS C 348 PHE 0.013 0.001 PHE D 990 TYR 0.010 0.001 TYR D1068 ARG 0.003 0.000 ARG D 114 Details of bonding type rmsd link_NAG-ASN : bond 0.01058 ( 7) link_NAG-ASN : angle 4.98436 ( 21) link_BETA1-4 : bond 0.00765 ( 8) link_BETA1-4 : angle 2.65858 ( 24) hydrogen bonds : bond 0.03781 ( 966) hydrogen bonds : angle 4.28286 ( 2775) SS BOND : bond 0.00154 ( 10) SS BOND : angle 1.00283 ( 20) covalent geometry : bond 0.00245 (21427) covalent geometry : angle 0.53749 (29034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7924 (tp30) cc_final: 0.7565 (tp30) REVERT: A 431 GLU cc_start: 0.8111 (tp30) cc_final: 0.7268 (tp30) REVERT: A 554 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8083 (mm-30) REVERT: A 571 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6813 (tpp) REVERT: A 760 GLU cc_start: 0.7962 (tp30) cc_final: 0.7689 (mm-30) REVERT: A 776 LYS cc_start: 0.6999 (mmtm) cc_final: 0.6709 (mmtm) REVERT: A 1245 MET cc_start: 0.8363 (tpt) cc_final: 0.8159 (tpt) REVERT: A 1258 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8210 (ttp) REVERT: A 1383 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7894 (mtm110) REVERT: A 1474 MET cc_start: 0.8397 (mmt) cc_final: 0.7963 (mmt) REVERT: A 1549 TRP cc_start: 0.6370 (OUTLIER) cc_final: 0.5765 (m-10) REVERT: D 43 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7260 (p0) REVERT: D 285 ASP cc_start: 0.8231 (m-30) cc_final: 0.7982 (m-30) REVERT: D 309 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: D 772 ASN cc_start: 0.8249 (m-40) cc_final: 0.7764 (p0) REVERT: C 58 LYS cc_start: 0.3422 (tppp) cc_final: 0.2986 (tptt) REVERT: C 334 ASP cc_start: 0.6637 (m-30) cc_final: 0.5909 (m-30) REVERT: C 351 GLU cc_start: 0.5786 (OUTLIER) cc_final: 0.5390 (tm-30) outliers start: 47 outliers final: 26 residues processed: 310 average time/residue: 0.3005 time to fit residues: 150.4560 Evaluate side-chains 300 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 267 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1258 MET Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1383 ARG Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1549 TRP Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 351 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN D 481 ASN D1062 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.178618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131590 restraints weight = 25330.371| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.97 r_work: 0.3084 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21452 Z= 0.158 Angle : 0.590 13.568 29099 Z= 0.288 Chirality : 0.044 0.268 3317 Planarity : 0.004 0.046 3637 Dihedral : 10.543 143.491 3477 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.90 % Favored : 94.06 % Rotamer: Outliers : 2.96 % Allowed : 17.46 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2524 helix: 0.94 (0.15), residues: 1205 sheet: -0.60 (0.31), residues: 279 loop : -1.49 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 185 HIS 0.004 0.001 HIS C 94 PHE 0.019 0.001 PHE D 990 TYR 0.016 0.001 TYR D 719 ARG 0.004 0.000 ARG D 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00960 ( 7) link_NAG-ASN : angle 4.78608 ( 21) link_BETA1-4 : bond 0.00697 ( 8) link_BETA1-4 : angle 2.83407 ( 24) hydrogen bonds : bond 0.03969 ( 966) hydrogen bonds : angle 4.24413 ( 2775) SS BOND : bond 0.00242 ( 10) SS BOND : angle 1.27743 ( 20) covalent geometry : bond 0.00379 (21427) covalent geometry : angle 0.56998 (29034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 279 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7923 (tp30) cc_final: 0.7549 (tp30) REVERT: A 431 GLU cc_start: 0.8080 (tp30) cc_final: 0.7219 (tp30) REVERT: A 571 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6770 (tpp) REVERT: A 760 GLU cc_start: 0.7992 (tp30) cc_final: 0.7722 (mm-30) REVERT: A 776 LYS cc_start: 0.6963 (mmtm) cc_final: 0.6571 (mmtm) REVERT: A 1033 LYS cc_start: 0.7202 (ptpp) cc_final: 0.6633 (mmtp) REVERT: A 1062 MET cc_start: 0.8607 (mtp) cc_final: 0.8355 (mtt) REVERT: A 1233 TRP cc_start: 0.7228 (t60) cc_final: 0.6949 (t60) REVERT: A 1258 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8143 (ttp) REVERT: A 1383 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7850 (mtm110) REVERT: A 1467 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8445 (pp30) REVERT: A 1474 MET cc_start: 0.8421 (mmt) cc_final: 0.8019 (mmt) REVERT: A 1549 TRP cc_start: 0.6355 (OUTLIER) cc_final: 0.5838 (m-10) REVERT: D 43 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7157 (p0) REVERT: D 309 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: D 704 ARG cc_start: 0.8276 (tpt90) cc_final: 0.7993 (tpt90) REVERT: D 772 ASN cc_start: 0.8284 (m-40) cc_final: 0.7759 (p0) REVERT: D 984 ASP cc_start: 0.8327 (t0) cc_final: 0.8123 (m-30) REVERT: C 58 LYS cc_start: 0.3410 (tppp) cc_final: 0.2986 (tptt) REVERT: C 93 LEU cc_start: 0.3340 (OUTLIER) cc_final: 0.3051 (mm) outliers start: 67 outliers final: 42 residues processed: 324 average time/residue: 0.2960 time to fit residues: 155.6125 Evaluate side-chains 312 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain A residue 1258 MET Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1383 ARG Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1549 TRP Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 1062 ASN Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 138 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 61 optimal weight: 0.0770 chunk 186 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.175929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.128555 restraints weight = 25142.291| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.05 r_work: 0.3098 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21452 Z= 0.248 Angle : 0.653 12.007 29099 Z= 0.320 Chirality : 0.046 0.274 3317 Planarity : 0.004 0.047 3637 Dihedral : 10.690 146.351 3477 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.54 % Favored : 93.42 % Rotamer: Outliers : 3.14 % Allowed : 17.86 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2524 helix: 0.71 (0.15), residues: 1215 sheet: -0.74 (0.31), residues: 276 loop : -1.58 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 185 HIS 0.006 0.001 HIS D 306 PHE 0.020 0.002 PHE D 990 TYR 0.017 0.002 TYR D 744 ARG 0.005 0.000 ARG D 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00938 ( 7) link_NAG-ASN : angle 4.82148 ( 21) link_BETA1-4 : bond 0.00688 ( 8) link_BETA1-4 : angle 3.05348 ( 24) hydrogen bonds : bond 0.04422 ( 966) hydrogen bonds : angle 4.34236 ( 2775) SS BOND : bond 0.00235 ( 10) SS BOND : angle 1.51941 ( 20) covalent geometry : bond 0.00609 (21427) covalent geometry : angle 0.63309 (29034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 269 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7955 (tp30) cc_final: 0.7595 (tp30) REVERT: A 554 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8229 (mm-30) REVERT: A 571 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6957 (ttp) REVERT: A 760 GLU cc_start: 0.8019 (tp30) cc_final: 0.7759 (mm-30) REVERT: A 1033 LYS cc_start: 0.7198 (ptpp) cc_final: 0.6682 (mmtp) REVERT: A 1258 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8142 (ttp) REVERT: A 1383 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7912 (mtm110) REVERT: A 1467 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8442 (pp30) REVERT: A 1474 MET cc_start: 0.8538 (mmt) cc_final: 0.8180 (mmt) REVERT: A 1544 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: A 1549 TRP cc_start: 0.6519 (OUTLIER) cc_final: 0.6102 (m-10) REVERT: D 43 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7145 (p0) REVERT: D 309 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: D 772 ASN cc_start: 0.8363 (m-40) cc_final: 0.7791 (p0) REVERT: C 58 LYS cc_start: 0.3471 (tppp) cc_final: 0.3032 (tptt) REVERT: C 93 LEU cc_start: 0.3206 (OUTLIER) cc_final: 0.2913 (mm) REVERT: C 334 ASP cc_start: 0.6626 (m-30) cc_final: 0.5914 (m-30) outliers start: 71 outliers final: 44 residues processed: 319 average time/residue: 0.2923 time to fit residues: 152.4556 Evaluate side-chains 314 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 261 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain A residue 1258 MET Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1383 ARG Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1544 GLU Chi-restraints excluded: chain A residue 1549 TRP Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 892 TYR Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 150 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 227 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.179932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.133224 restraints weight = 24907.060| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.02 r_work: 0.3127 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21452 Z= 0.118 Angle : 0.570 12.954 29099 Z= 0.277 Chirality : 0.042 0.275 3317 Planarity : 0.003 0.046 3637 Dihedral : 10.216 140.611 3477 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.47 % Favored : 94.49 % Rotamer: Outliers : 2.56 % Allowed : 18.70 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2524 helix: 1.06 (0.15), residues: 1192 sheet: -0.63 (0.31), residues: 271 loop : -1.43 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1233 HIS 0.004 0.001 HIS A 925 PHE 0.018 0.001 PHE D 990 TYR 0.009 0.001 TYR D 764 ARG 0.003 0.000 ARG A 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00953 ( 7) link_NAG-ASN : angle 4.64382 ( 21) link_BETA1-4 : bond 0.00759 ( 8) link_BETA1-4 : angle 2.69138 ( 24) hydrogen bonds : bond 0.03583 ( 966) hydrogen bonds : angle 4.13776 ( 2775) SS BOND : bond 0.00099 ( 10) SS BOND : angle 1.08678 ( 20) covalent geometry : bond 0.00268 (21427) covalent geometry : angle 0.55083 (29034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 280 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 ILE cc_start: 0.8301 (pt) cc_final: 0.8040 (pt) REVERT: A 213 GLU cc_start: 0.7957 (tp30) cc_final: 0.7572 (tp30) REVERT: A 571 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6672 (tpp) REVERT: A 760 GLU cc_start: 0.7982 (tp30) cc_final: 0.7749 (mm-30) REVERT: A 776 LYS cc_start: 0.6927 (mmtm) cc_final: 0.6412 (mmtm) REVERT: A 1033 LYS cc_start: 0.7287 (ptpp) cc_final: 0.6710 (mmtp) REVERT: A 1062 MET cc_start: 0.8731 (mtp) cc_final: 0.8519 (mtt) REVERT: A 1245 MET cc_start: 0.8272 (tpt) cc_final: 0.8051 (tpt) REVERT: A 1258 MET cc_start: 0.8327 (ttp) cc_final: 0.7987 (ttp) REVERT: A 1383 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7772 (mtm110) REVERT: A 1467 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8352 (pp30) REVERT: A 1474 MET cc_start: 0.8420 (mmt) cc_final: 0.8005 (mmt) REVERT: A 1549 TRP cc_start: 0.6518 (OUTLIER) cc_final: 0.6013 (m-10) REVERT: D 41 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8498 (tm-30) REVERT: D 43 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7116 (p0) REVERT: D 195 LYS cc_start: 0.8930 (tmtt) cc_final: 0.8554 (tmtt) REVERT: D 309 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: D 719 TYR cc_start: 0.7533 (t80) cc_final: 0.7216 (t80) REVERT: D 772 ASN cc_start: 0.8307 (m-40) cc_final: 0.7731 (p0) REVERT: C 58 LYS cc_start: 0.3554 (tppp) cc_final: 0.3170 (tptt) REVERT: C 93 LEU cc_start: 0.3372 (OUTLIER) cc_final: 0.3098 (mm) REVERT: C 334 ASP cc_start: 0.6495 (m-30) cc_final: 0.5802 (m-30) outliers start: 58 outliers final: 38 residues processed: 320 average time/residue: 0.2977 time to fit residues: 153.4731 Evaluate side-chains 310 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 265 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1383 ARG Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1549 TRP Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 892 TYR Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 154 optimal weight: 0.7980 chunk 214 optimal weight: 0.0970 chunk 234 optimal weight: 0.4980 chunk 194 optimal weight: 1.9990 chunk 165 optimal weight: 0.0980 chunk 125 optimal weight: 0.0970 chunk 239 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1062 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.181996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134848 restraints weight = 25227.541| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.94 r_work: 0.3203 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21452 Z= 0.101 Angle : 0.563 13.686 29099 Z= 0.272 Chirality : 0.042 0.284 3317 Planarity : 0.003 0.046 3637 Dihedral : 9.806 134.859 3477 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.19 % Favored : 94.77 % Rotamer: Outliers : 2.34 % Allowed : 18.74 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2524 helix: 1.24 (0.15), residues: 1195 sheet: -0.61 (0.31), residues: 271 loop : -1.33 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1233 HIS 0.005 0.001 HIS A 925 PHE 0.013 0.001 PHE D 990 TYR 0.009 0.001 TYR D 744 ARG 0.005 0.000 ARG A 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00948 ( 7) link_NAG-ASN : angle 4.47635 ( 21) link_BETA1-4 : bond 0.00630 ( 8) link_BETA1-4 : angle 2.60128 ( 24) hydrogen bonds : bond 0.03246 ( 966) hydrogen bonds : angle 4.00477 ( 2775) SS BOND : bond 0.00198 ( 10) SS BOND : angle 0.88285 ( 20) covalent geometry : bond 0.00215 (21427) covalent geometry : angle 0.54494 (29034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7893 (tp30) cc_final: 0.7489 (tp30) REVERT: A 439 ASP cc_start: 0.7252 (p0) cc_final: 0.6599 (t0) REVERT: A 571 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6631 (tpp) REVERT: A 760 GLU cc_start: 0.7922 (tp30) cc_final: 0.7699 (mm-30) REVERT: A 776 LYS cc_start: 0.6791 (mmtm) cc_final: 0.6299 (mmtm) REVERT: A 1033 LYS cc_start: 0.7184 (ptpp) cc_final: 0.6634 (mmtp) REVERT: A 1062 MET cc_start: 0.8792 (mtp) cc_final: 0.8576 (mtt) REVERT: A 1245 MET cc_start: 0.8245 (tpt) cc_final: 0.7957 (tpt) REVERT: A 1258 MET cc_start: 0.8235 (ttp) cc_final: 0.7963 (ttp) REVERT: A 1383 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7687 (mtm110) REVERT: A 1467 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8311 (pp30) REVERT: A 1474 MET cc_start: 0.8210 (mmt) cc_final: 0.7791 (mmt) REVERT: A 1549 TRP cc_start: 0.6398 (OUTLIER) cc_final: 0.5910 (m-10) REVERT: D 41 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8525 (tm-30) REVERT: D 43 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7085 (p0) REVERT: D 195 LYS cc_start: 0.8892 (tmtt) cc_final: 0.8528 (tmtt) REVERT: D 285 ASP cc_start: 0.8298 (m-30) cc_final: 0.8071 (m-30) REVERT: D 309 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: D 704 ARG cc_start: 0.8192 (tpt90) cc_final: 0.7988 (tpt90) REVERT: D 719 TYR cc_start: 0.7475 (t80) cc_final: 0.7205 (t80) REVERT: D 772 ASN cc_start: 0.8310 (m-40) cc_final: 0.7740 (p0) REVERT: C 58 LYS cc_start: 0.3550 (tppp) cc_final: 0.3147 (tptt) REVERT: C 93 LEU cc_start: 0.3455 (OUTLIER) cc_final: 0.3197 (mm) REVERT: C 334 ASP cc_start: 0.6485 (m-30) cc_final: 0.5683 (m-30) outliers start: 53 outliers final: 35 residues processed: 314 average time/residue: 0.3280 time to fit residues: 164.9058 Evaluate side-chains 305 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1383 ARG Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1549 TRP Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 892 TYR Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 984 ASP Chi-restraints excluded: chain D residue 1062 ASN Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 216 optimal weight: 0.0170 chunk 182 optimal weight: 4.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.178798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131369 restraints weight = 25204.171| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.00 r_work: 0.3133 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21452 Z= 0.171 Angle : 0.613 14.628 29099 Z= 0.299 Chirality : 0.044 0.267 3317 Planarity : 0.004 0.046 3637 Dihedral : 9.896 137.241 3477 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.86 % Favored : 94.10 % Rotamer: Outliers : 2.08 % Allowed : 19.23 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2524 helix: 1.15 (0.15), residues: 1193 sheet: -0.64 (0.31), residues: 271 loop : -1.41 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1233 HIS 0.004 0.001 HIS D 306 PHE 0.017 0.001 PHE A1306 TYR 0.012 0.001 TYR A 719 ARG 0.006 0.000 ARG A 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00899 ( 7) link_NAG-ASN : angle 4.39374 ( 21) link_BETA1-4 : bond 0.00676 ( 8) link_BETA1-4 : angle 2.84822 ( 24) hydrogen bonds : bond 0.03771 ( 966) hydrogen bonds : angle 4.08840 ( 2775) SS BOND : bond 0.00185 ( 10) SS BOND : angle 1.26290 ( 20) covalent geometry : bond 0.00412 (21427) covalent geometry : angle 0.59595 (29034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7956 (tp30) cc_final: 0.7554 (tp30) REVERT: A 439 ASP cc_start: 0.7251 (p0) cc_final: 0.6600 (t0) REVERT: A 571 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6732 (tpp) REVERT: A 587 LEU cc_start: 0.8344 (tp) cc_final: 0.8051 (tt) REVERT: A 760 GLU cc_start: 0.7960 (tp30) cc_final: 0.7723 (mm-30) REVERT: A 776 LYS cc_start: 0.6891 (mmtm) cc_final: 0.6593 (mmtm) REVERT: A 1033 LYS cc_start: 0.7274 (ptpp) cc_final: 0.6700 (mmtp) REVERT: A 1245 MET cc_start: 0.8302 (tpt) cc_final: 0.8077 (tpt) REVERT: A 1383 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7785 (mtm110) REVERT: A 1467 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8392 (pp30) REVERT: A 1474 MET cc_start: 0.8421 (mmt) cc_final: 0.8036 (mmt) REVERT: A 1529 TYR cc_start: 0.8995 (t80) cc_final: 0.8700 (t80) REVERT: A 1544 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7205 (pt0) REVERT: D 41 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8467 (tm-30) REVERT: D 43 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7106 (p0) REVERT: D 195 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8554 (tmtt) REVERT: D 309 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: D 678 GLU cc_start: 0.7753 (pm20) cc_final: 0.7168 (pm20) REVERT: D 704 ARG cc_start: 0.8247 (tpt90) cc_final: 0.8016 (tpt90) REVERT: D 719 TYR cc_start: 0.7542 (t80) cc_final: 0.7315 (t80) REVERT: D 772 ASN cc_start: 0.8348 (m-40) cc_final: 0.7779 (p0) REVERT: C 58 LYS cc_start: 0.3522 (tppp) cc_final: 0.3134 (tptt) REVERT: C 93 LEU cc_start: 0.3514 (OUTLIER) cc_final: 0.3243 (mm) REVERT: C 334 ASP cc_start: 0.6429 (m-30) cc_final: 0.5712 (m-30) outliers start: 47 outliers final: 35 residues processed: 301 average time/residue: 0.4346 time to fit residues: 214.0362 Evaluate side-chains 308 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 5.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1383 ARG Chi-restraints excluded: chain A residue 1427 MET Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1544 GLU Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 892 TYR Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 133 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.180622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.133487 restraints weight = 25111.791| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.00 r_work: 0.3167 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21452 Z= 0.115 Angle : 0.583 16.729 29099 Z= 0.281 Chirality : 0.043 0.278 3317 Planarity : 0.003 0.046 3637 Dihedral : 9.645 135.920 3477 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 1.90 % Allowed : 19.58 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2524 helix: 1.21 (0.15), residues: 1196 sheet: -0.61 (0.31), residues: 271 loop : -1.36 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1549 HIS 0.004 0.001 HIS A 925 PHE 0.015 0.001 PHE D 990 TYR 0.008 0.001 TYR A 719 ARG 0.006 0.000 ARG A 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00923 ( 7) link_NAG-ASN : angle 4.36887 ( 21) link_BETA1-4 : bond 0.00722 ( 8) link_BETA1-4 : angle 2.70042 ( 24) hydrogen bonds : bond 0.03423 ( 966) hydrogen bonds : angle 4.01897 ( 2775) SS BOND : bond 0.00155 ( 10) SS BOND : angle 1.01777 ( 20) covalent geometry : bond 0.00263 (21427) covalent geometry : angle 0.56543 (29034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7916 (tp30) cc_final: 0.7501 (tp30) REVERT: A 439 ASP cc_start: 0.7244 (p0) cc_final: 0.6595 (t0) REVERT: A 571 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6663 (tpp) REVERT: A 587 LEU cc_start: 0.8329 (tp) cc_final: 0.8013 (tt) REVERT: A 760 GLU cc_start: 0.7904 (tp30) cc_final: 0.7669 (mm-30) REVERT: A 776 LYS cc_start: 0.6763 (mmtm) cc_final: 0.6485 (mmtm) REVERT: A 1033 LYS cc_start: 0.7247 (ptpp) cc_final: 0.6660 (mmtp) REVERT: A 1062 MET cc_start: 0.8745 (mtp) cc_final: 0.8513 (mtt) REVERT: A 1245 MET cc_start: 0.8245 (tpt) cc_final: 0.8028 (tpt) REVERT: A 1258 MET cc_start: 0.8385 (ttp) cc_final: 0.8064 (ttp) REVERT: A 1383 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7715 (mtm110) REVERT: A 1467 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8340 (pp30) REVERT: A 1474 MET cc_start: 0.8337 (mmt) cc_final: 0.7945 (mmt) REVERT: A 1544 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7284 (pt0) REVERT: D 41 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 43 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7066 (p0) REVERT: D 195 LYS cc_start: 0.8943 (tmtt) cc_final: 0.8534 (tmtt) REVERT: D 285 ASP cc_start: 0.8414 (m-30) cc_final: 0.8166 (m-30) REVERT: D 309 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: D 678 GLU cc_start: 0.7786 (pm20) cc_final: 0.7314 (pm20) REVERT: D 719 TYR cc_start: 0.7488 (t80) cc_final: 0.7278 (t80) REVERT: D 772 ASN cc_start: 0.8322 (m-40) cc_final: 0.7746 (p0) REVERT: C 58 LYS cc_start: 0.3587 (tppp) cc_final: 0.3166 (tptt) REVERT: C 93 LEU cc_start: 0.3437 (OUTLIER) cc_final: 0.3186 (mm) REVERT: C 334 ASP cc_start: 0.6524 (m-30) cc_final: 0.5795 (m-30) outliers start: 43 outliers final: 35 residues processed: 298 average time/residue: 0.3085 time to fit residues: 148.4609 Evaluate side-chains 310 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1383 ARG Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1544 GLU Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 892 TYR Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 99 optimal weight: 0.7980 chunk 4 optimal weight: 0.0770 chunk 174 optimal weight: 0.0470 chunk 130 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 175 optimal weight: 0.5980 chunk 208 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.9038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1062 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.181331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134433 restraints weight = 25160.143| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.95 r_work: 0.3137 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21452 Z= 0.115 Angle : 0.583 18.266 29099 Z= 0.280 Chirality : 0.043 0.277 3317 Planarity : 0.003 0.046 3637 Dihedral : 9.456 134.365 3477 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.03 % Allowed : 19.50 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2524 helix: 1.25 (0.15), residues: 1195 sheet: -0.60 (0.31), residues: 271 loop : -1.35 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 185 HIS 0.003 0.001 HIS D 306 PHE 0.015 0.001 PHE D 990 TYR 0.009 0.001 TYR D 744 ARG 0.006 0.000 ARG A 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00908 ( 7) link_NAG-ASN : angle 4.31949 ( 21) link_BETA1-4 : bond 0.00707 ( 8) link_BETA1-4 : angle 2.71799 ( 24) hydrogen bonds : bond 0.03371 ( 966) hydrogen bonds : angle 3.98264 ( 2775) SS BOND : bond 0.00161 ( 10) SS BOND : angle 1.00707 ( 20) covalent geometry : bond 0.00262 (21427) covalent geometry : angle 0.56616 (29034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18295.23 seconds wall clock time: 320 minutes 13.17 seconds (19213.17 seconds total)