Starting phenix.real_space_refine on Thu Feb 5 04:39:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kz6_62652/02_2026/9kz6_62652.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kz6_62652/02_2026/9kz6_62652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kz6_62652/02_2026/9kz6_62652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kz6_62652/02_2026/9kz6_62652.map" model { file = "/net/cci-nas-00/data/ceres_data/9kz6_62652/02_2026/9kz6_62652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kz6_62652/02_2026/9kz6_62652.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 9283 2.51 5 N 2391 2.21 5 O 2805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14536 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 14204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1771, 14204 Classifications: {'peptide': 1771} Link IDs: {'CIS': 3, 'PCIS': 7, 'PTRANS': 101, 'TRANS': 1659} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "D" 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: "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: 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: "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: "I" 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: "J" 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: "K" 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: "L" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.33, per 1000 atoms: 0.23 Number of scatterers: 14536 At special positions: 0 Unit cell: (154, 116.16, 110, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2805 8.00 N 2391 7.00 C 9283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 84 " distance=2.04 Simple disulfide: pdb=" SG CYS A 626 " - pdb=" SG CYS A 637 " distance=2.03 Simple disulfide: pdb=" SG CYS A 933 " - pdb=" SG CYS A 950 " distance=2.06 Simple disulfide: pdb=" SG CYS A 945 " - pdb=" SG CYS A 963 " distance=2.01 Simple disulfide: pdb=" SG CYS A1524 " - pdb=" SG CYS A1535 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1901 " - " ASN A1570 " " NAG B 1 " - " ASN A 424 " " NAG C 1 " - " ASN A 674 " " NAG D 1 " - " ASN A 916 " " NAG E 1 " - " ASN A1222 " " NAG F 1 " - " ASN A1290 " " NAG G 1 " - " ASN A1331 " " NAG H 1 " - " ASN A1355 " " NAG I 1 " - " ASN A1565 " " NAG J 1 " - " ASN A1639 " " NAG K 1 " - " ASN A1737 " " NAG L 1 " - " ASN A1804 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 532.0 milliseconds 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 25 sheets defined 24.2% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 75 through 83 Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 356 through 370 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 399 through 409 Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 470 through 486 removed outlier: 3.519A pdb=" N THR A 474 " --> pdb=" O ASN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.723A pdb=" N THR A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 588 removed outlier: 3.571A pdb=" N LYS A 587 " --> pdb=" O GLY A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 616 removed outlier: 4.479A pdb=" N ILE A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Proline residue: A 608 - end of helix Processing helix chain 'A' and resid 633 through 645 removed outlier: 3.561A pdb=" N VAL A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 Processing helix chain 'A' and resid 670 through 686 Processing helix chain 'A' and resid 686 through 701 Processing helix chain 'A' and resid 707 through 711 Processing helix chain 'A' and resid 796 through 801 Processing helix chain 'A' and resid 941 through 949 Processing helix chain 'A' and resid 990 through 997 Processing helix chain 'A' and resid 1191 through 1201 Processing helix chain 'A' and resid 1207 through 1212 Processing helix chain 'A' and resid 1222 through 1236 removed outlier: 3.923A pdb=" N ILE A1226 " --> pdb=" O ASN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1254 removed outlier: 5.254A pdb=" N GLU A1251 " --> pdb=" O ASP A1248 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG A1252 " --> pdb=" O TYR A1249 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A1253 " --> pdb=" O MET A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1263 Processing helix chain 'A' and resid 1264 through 1275 Processing helix chain 'A' and resid 1295 through 1304 Processing helix chain 'A' and resid 1335 through 1343 Processing helix chain 'A' and resid 1354 through 1370 Processing helix chain 'A' and resid 1374 through 1378 Processing helix chain 'A' and resid 1405 through 1410 Processing helix chain 'A' and resid 1445 through 1449 Processing helix chain 'A' and resid 1451 through 1469 removed outlier: 4.273A pdb=" N ARG A1458 " --> pdb=" O TRP A1454 " (cutoff:3.500A) Proline residue: A1459 - end of helix Processing helix chain 'A' and resid 1499 through 1514 removed outlier: 3.600A pdb=" N ILE A1505 " --> pdb=" O LEU A1501 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1543 Processing helix chain 'A' and resid 1560 through 1564 removed outlier: 4.135A pdb=" N TRP A1564 " --> pdb=" O PRO A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1597 Proline residue: A1584 - end of helix Processing helix chain 'A' and resid 1611 through 1617 removed outlier: 3.560A pdb=" N ASP A1616 " --> pdb=" O VAL A1613 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1617 " --> pdb=" O THR A1614 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1697 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107 removed outlier: 6.630A pdb=" N ARG A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A 288 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N THR A 271 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE A 272 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLY A 232 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 274 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 230 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 187 removed outlier: 6.962A pdb=" N ILE A 193 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP A 206 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 195 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 215 removed outlier: 3.774A pdb=" N PHE A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 621 through 622 removed outlier: 7.056A pdb=" N HIS A 591 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TRP A 592 " --> pdb=" O THR A 578 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU A 414 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N TRP A 494 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 416 " --> pdb=" O TRP A 494 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE A 347 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N HIS A 378 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU A 349 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N HIS A 348 " --> pdb=" O ASN A 652 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N ASN A 654 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER A 350 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS A 653 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 706 removed outlier: 3.531A pdb=" N LEU A 731 " --> pdb=" O TRP A 727 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 743 through 748 Processing sheet with id=AB1, first strand: chain 'A' and resid 786 through 791 removed outlier: 6.468A pdb=" N LEU A 805 " --> pdb=" O PHE A 866 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 868 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 903 " --> pdb=" O ASP A 898 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 786 through 791 removed outlier: 6.468A pdb=" N LEU A 805 " --> pdb=" O PHE A 866 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 868 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 817 through 823 removed outlier: 3.505A pdb=" N LEU A 821 " --> pdb=" O TYR A 840 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 839 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 817 through 823 removed outlier: 3.505A pdb=" N LEU A 821 " --> pdb=" O TYR A 840 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 918 " --> pdb=" O VAL A 882 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL A 882 " --> pdb=" O THR A 918 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU A 920 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL A 880 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 951 through 952 Processing sheet with id=AB6, first strand: chain 'A' and resid 970 through 977 removed outlier: 4.385A pdb=" N VAL A 975 " --> pdb=" O THR A 983 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A 983 " --> pdb=" O VAL A 975 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TYR A 977 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY A 981 " --> pdb=" O TYR A 977 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A1012 " --> pdb=" O MET A1016 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET A1016 " --> pdb=" O HIS A1012 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A1102 " --> pdb=" O HIS A1137 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYR A1139 " --> pdb=" O GLY A1100 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY A1100 " --> pdb=" O TYR A1139 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET A1141 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU A1098 " --> pdb=" O MET A1141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1050 through 1055 removed outlier: 3.515A pdb=" N GLY A1060 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG A1065 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A1071 " --> pdb=" O ARG A1065 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB9, first strand: chain 'A' and resid 1519 through 1520 removed outlier: 6.984A pdb=" N HIS A1489 " --> pdb=" O GLY A1520 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A1474 " --> pdb=" O GLY A1488 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TRP A1490 " --> pdb=" O ILE A1474 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER A1476 " --> pdb=" O TRP A1490 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A1383 " --> pdb=" O VAL A1279 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A1281 " --> pdb=" O GLY A1383 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A1280 " --> pdb=" O GLN A1243 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A1282 " --> pdb=" O SER A1245 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU A1215 " --> pdb=" O TYR A1244 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN A1214 " --> pdb=" O ASN A1550 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1287 through 1288 Processing sheet with id=AC2, first strand: chain 'A' and resid 1434 through 1436 Processing sheet with id=AC3, first strand: chain 'A' and resid 1601 through 1602 removed outlier: 4.242A pdb=" N ASN A1675 " --> pdb=" O SER A1630 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TRP A1649 " --> pdb=" O ILE A1658 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1639 through 1644 Processing sheet with id=AC5, first strand: chain 'A' and resid 1682 through 1687 removed outlier: 5.862A pdb=" N MET A1701 " --> pdb=" O LEU A1763 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A1765 " --> pdb=" O MET A1701 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1682 through 1687 removed outlier: 5.862A pdb=" N MET A1701 " --> pdb=" O LEU A1763 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A1765 " --> pdb=" O MET A1701 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU A1810 " --> pdb=" O LEU A1763 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1713 through 1719 removed outlier: 6.602A pdb=" N ASN A1737 " --> pdb=" O VAL A1749 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N VAL A1749 " --> pdb=" O ASN A1737 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER A1739 " --> pdb=" O SER A1747 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N SER A1747 " --> pdb=" O SER A1739 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N SER A1741 " --> pdb=" O MET A1745 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N MET A1745 " --> pdb=" O SER A1741 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER A1816 " --> pdb=" O SER A1747 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A1817 " --> pdb=" O SER A1782 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1446 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: 4.46 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2380 1.30 - 1.43: 4302 1.43 - 1.56: 8183 1.56 - 1.69: 0 1.69 - 1.82: 93 Bond restraints: 14958 Sorted by residual: bond pdb=" C LEU A 122 " pdb=" N LYS A 123 " ideal model delta sigma weight residual 1.329 1.237 0.091 1.36e-02 5.41e+03 4.52e+01 bond pdb=" C TYR A 231 " pdb=" O TYR A 231 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.22e-02 6.72e+03 2.73e+01 bond pdb=" N ILE A1238 " pdb=" CA ILE A1238 " ideal model delta sigma weight residual 1.460 1.495 -0.034 7.30e-03 1.88e+04 2.20e+01 bond pdb=" C LYS A 123 " pdb=" N ARG A 124 " ideal model delta sigma weight residual 1.330 1.265 0.065 1.42e-02 4.96e+03 2.10e+01 bond pdb=" CA SER A1122 " pdb=" CB SER A1122 " ideal model delta sigma weight residual 1.531 1.457 0.074 1.65e-02 3.67e+03 2.00e+01 ... (remaining 14953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 17436 2.15 - 4.30: 2661 4.30 - 6.46: 265 6.46 - 8.61: 41 8.61 - 10.76: 5 Bond angle restraints: 20408 Sorted by residual: angle pdb=" N ILE A1226 " pdb=" CA ILE A1226 " pdb=" C ILE A1226 " ideal model delta sigma weight residual 110.72 104.22 6.50 1.01e+00 9.80e-01 4.14e+01 angle pdb=" N TYR A 897 " pdb=" CA TYR A 897 " pdb=" CB TYR A 897 " ideal model delta sigma weight residual 110.68 100.54 10.14 1.68e+00 3.54e-01 3.64e+01 angle pdb=" CA TYR A 231 " pdb=" C TYR A 231 " pdb=" O TYR A 231 " ideal model delta sigma weight residual 120.66 113.75 6.91 1.15e+00 7.56e-01 3.61e+01 angle pdb=" N TYR A 231 " pdb=" CA TYR A 231 " pdb=" CB TYR A 231 " ideal model delta sigma weight residual 111.00 100.24 10.76 1.81e+00 3.05e-01 3.53e+01 angle pdb=" CA PHE A1792 " pdb=" CB PHE A1792 " pdb=" CG PHE A1792 " ideal model delta sigma weight residual 113.80 119.69 -5.89 1.00e+00 1.00e+00 3.47e+01 ... (remaining 20403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.40: 8559 24.40 - 48.80: 377 48.80 - 73.20: 117 73.20 - 97.59: 10 97.59 - 121.99: 1 Dihedral angle restraints: 9064 sinusoidal: 3898 harmonic: 5166 Sorted by residual: dihedral pdb=" CA SER A1400 " pdb=" C SER A1400 " pdb=" N PRO A1401 " pdb=" CA PRO A1401 " ideal model delta harmonic sigma weight residual 180.00 58.01 121.99 0 5.00e+00 4.00e-02 5.95e+02 dihedral pdb=" CD ARG A1217 " pdb=" NE ARG A1217 " pdb=" CZ ARG A1217 " pdb=" NH1 ARG A1217 " ideal model delta sinusoidal sigma weight residual 0.00 -87.14 87.14 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS A 933 " pdb=" SG CYS A 933 " pdb=" SG CYS A 950 " pdb=" CB CYS A 950 " ideal model delta sinusoidal sigma weight residual -86.00 -5.86 -80.14 1 1.00e+01 1.00e-02 7.96e+01 ... (remaining 9061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1223 0.065 - 0.130: 720 0.130 - 0.195: 235 0.195 - 0.260: 53 0.260 - 0.325: 5 Chirality restraints: 2236 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.08e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.46e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.85e+01 ... (remaining 2233 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1639 " -0.142 2.00e-02 2.50e+03 1.65e-01 3.41e+02 pdb=" CG ASN A1639 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN A1639 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A1639 " 0.271 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1217 " -1.108 9.50e-02 1.11e+02 4.96e-01 1.49e+02 pdb=" NE ARG A1217 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A1217 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A1217 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A1217 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1804 " -0.096 2.00e-02 2.50e+03 1.05e-01 1.38e+02 pdb=" CG ASN A1804 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN A1804 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A1804 " 0.166 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " -0.127 2.00e-02 2.50e+03 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2852 2.79 - 3.32: 12940 3.32 - 3.85: 24199 3.85 - 4.37: 30755 4.37 - 4.90: 50740 Nonbonded interactions: 121486 Sorted by model distance: nonbonded pdb=" NH1 ARG A 366 " pdb=" OG SER A 665 " model vdw 2.266 3.120 nonbonded pdb=" OD2 ASP A 715 " pdb=" OH TYR A 747 " model vdw 2.312 3.040 nonbonded pdb=" O ASP A1611 " pdb=" OG1 THR A1614 " model vdw 2.370 3.040 nonbonded pdb=" O SER A 856 " pdb=" OG SER A 856 " model vdw 2.383 3.040 nonbonded pdb=" O ALA A1236 " pdb=" NH1 ARG A1573 " model vdw 2.391 3.120 ... (remaining 121481 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 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.900 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 0.012 0.091 14987 Z= 0.819 Angle : 1.594 26.350 20490 Z= 1.069 Chirality : 0.087 0.325 2236 Planarity : 0.030 0.496 2628 Dihedral : 14.617 121.993 5749 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.97 % Favored : 94.74 % Rotamer: Outliers : 2.97 % Allowed : 8.07 % Favored : 88.96 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.12 % Twisted Proline : 0.93 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.18), residues: 1769 helix: -0.84 (0.24), residues: 366 sheet: -0.16 (0.25), residues: 445 loop : -1.72 (0.17), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 149 TYR 0.043 0.004 TYR A1682 PHE 0.026 0.004 PHE A 613 TRP 0.048 0.005 TRP A 753 HIS 0.011 0.002 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.01169 (14958) covalent geometry : angle 1.53790 (20408) SS BOND : bond 0.01725 ( 5) SS BOND : angle 6.55304 ( 10) hydrogen bonds : bond 0.23219 ( 522) hydrogen bonds : angle 7.85628 ( 1446) link_BETA1-4 : bond 0.04207 ( 11) link_BETA1-4 : angle 8.94404 ( 33) link_BETA1-6 : bond 0.03350 ( 1) link_BETA1-6 : angle 4.33306 ( 3) link_NAG-ASN : bond 0.00607 ( 12) link_NAG-ASN : angle 4.28123 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.6253 (mm-40) cc_final: 0.5276 (mp-120) REVERT: A 185 MET cc_start: 0.7349 (ttp) cc_final: 0.6820 (mmt) REVERT: A 329 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6913 (mm-30) REVERT: A 389 ASP cc_start: 0.7511 (m-30) cc_final: 0.7106 (m-30) REVERT: A 442 LYS cc_start: 0.7702 (mtpt) cc_final: 0.7479 (mmtp) REVERT: A 443 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7022 (pp) REVERT: A 537 MET cc_start: 0.7728 (mmp) cc_final: 0.7479 (mmt) REVERT: A 641 MET cc_start: 0.8237 (mmm) cc_final: 0.8035 (tpp) REVERT: A 742 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6856 (mt-10) REVERT: A 868 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7021 (tt0) REVERT: A 920 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6781 (mt-10) REVERT: A 974 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6488 (t0) REVERT: A 1076 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: A 1131 MET cc_start: 0.7341 (mtt) cc_final: 0.6976 (mtp) REVERT: A 1218 TYR cc_start: 0.7056 (t80) cc_final: 0.6815 (t80) REVERT: A 1225 GLU cc_start: 0.5744 (OUTLIER) cc_final: 0.5374 (tt0) REVERT: A 1271 ARG cc_start: 0.5714 (ttt180) cc_final: 0.5475 (mtm110) REVERT: A 1309 LYS cc_start: 0.7545 (mtmt) cc_final: 0.7307 (mtmm) REVERT: A 1373 GLN cc_start: 0.6452 (mm-40) cc_final: 0.5777 (mp10) REVERT: A 1388 MET cc_start: 0.7963 (mmm) cc_final: 0.7406 (mmt) REVERT: A 1558 ARG cc_start: 0.4744 (mtp180) cc_final: 0.4515 (mtm-85) REVERT: A 1592 MET cc_start: 0.7038 (mmp) cc_final: 0.6782 (mmp) REVERT: A 1596 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7285 (mt-10) REVERT: A 1666 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7429 (t70) REVERT: A 1822 SER cc_start: 0.6777 (p) cc_final: 0.6576 (t) outliers start: 46 outliers final: 7 residues processed: 218 average time/residue: 0.1444 time to fit residues: 44.7010 Evaluate side-chains 108 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1111 ARG Chi-restraints excluded: chain A residue 1224 SER Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1403 CYS Chi-restraints excluded: chain A residue 1406 SER Chi-restraints excluded: chain A residue 1666 ASP Chi-restraints excluded: chain A residue 1768 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 106 GLN ** A1106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS A1165 GLN A1373 GLN ** A1550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1723 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.081402 restraints weight = 23534.825| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.66 r_work: 0.2775 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14987 Z= 0.170 Angle : 0.705 12.713 20490 Z= 0.358 Chirality : 0.048 0.237 2236 Planarity : 0.005 0.053 2628 Dihedral : 6.705 59.993 2471 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 1.36 % Allowed : 9.62 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1769 helix: 0.65 (0.27), residues: 366 sheet: 0.26 (0.25), residues: 441 loop : -1.24 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1344 TYR 0.021 0.002 TYR A1461 PHE 0.020 0.002 PHE A1019 TRP 0.019 0.001 TRP A1322 HIS 0.005 0.001 HIS A1794 Details of bonding type rmsd covalent geometry : bond 0.00395 (14958) covalent geometry : angle 0.68032 (20408) SS BOND : bond 0.00351 ( 5) SS BOND : angle 1.74699 ( 10) hydrogen bonds : bond 0.05848 ( 522) hydrogen bonds : angle 5.70909 ( 1446) link_BETA1-4 : bond 0.00868 ( 11) link_BETA1-4 : angle 3.72448 ( 33) link_BETA1-6 : bond 0.00160 ( 1) link_BETA1-6 : angle 1.60592 ( 3) link_NAG-ASN : bond 0.00537 ( 12) link_NAG-ASN : angle 2.61170 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8026 (p90) cc_final: 0.7793 (p90) REVERT: A 159 GLN cc_start: 0.6603 (mm-40) cc_final: 0.6072 (mp-120) REVERT: A 451 VAL cc_start: 0.7520 (OUTLIER) cc_final: 0.7293 (t) REVERT: A 898 ASP cc_start: 0.7725 (t70) cc_final: 0.7305 (t0) REVERT: A 1004 SER cc_start: 0.8434 (t) cc_final: 0.8232 (p) REVERT: A 1017 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8888 (pt) REVERT: A 1271 ARG cc_start: 0.7065 (ttt180) cc_final: 0.6682 (mtm110) REVERT: A 1309 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8266 (mtmm) REVERT: A 1388 MET cc_start: 0.8687 (mmm) cc_final: 0.8101 (mmt) REVERT: A 1534 MET cc_start: 0.8448 (ttp) cc_final: 0.8073 (ttp) REVERT: A 1558 ARG cc_start: 0.5778 (mtp180) cc_final: 0.5351 (mtm180) REVERT: A 1590 MET cc_start: 0.9210 (mmp) cc_final: 0.8987 (mmt) REVERT: A 1592 MET cc_start: 0.8839 (mmp) cc_final: 0.8583 (mmp) outliers start: 21 outliers final: 11 residues processed: 126 average time/residue: 0.1180 time to fit residues: 22.7936 Evaluate side-chains 100 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1403 CYS Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1768 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 161 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 15 optimal weight: 0.0170 chunk 114 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 106 GLN A1116 HIS A1550 ASN A1675 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.080243 restraints weight = 23541.556| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.72 r_work: 0.2752 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14987 Z= 0.149 Angle : 0.624 10.581 20490 Z= 0.317 Chirality : 0.047 0.236 2236 Planarity : 0.005 0.060 2628 Dihedral : 5.912 56.766 2454 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.81 % Allowed : 10.01 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1769 helix: 1.15 (0.28), residues: 372 sheet: 0.38 (0.25), residues: 431 loop : -1.16 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.016 0.002 TYR A1461 PHE 0.021 0.002 PHE A1019 TRP 0.019 0.001 TRP A1322 HIS 0.005 0.001 HIS A 678 Details of bonding type rmsd covalent geometry : bond 0.00349 (14958) covalent geometry : angle 0.60742 (20408) SS BOND : bond 0.00195 ( 5) SS BOND : angle 1.25316 ( 10) hydrogen bonds : bond 0.05291 ( 522) hydrogen bonds : angle 5.26315 ( 1446) link_BETA1-4 : bond 0.00863 ( 11) link_BETA1-4 : angle 2.97656 ( 33) link_BETA1-6 : bond 0.00366 ( 1) link_BETA1-6 : angle 1.07059 ( 3) link_NAG-ASN : bond 0.00426 ( 12) link_NAG-ASN : angle 1.90084 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.6682 (mm-40) cc_final: 0.6154 (mp-120) REVERT: A 387 ARG cc_start: 0.8182 (mpt-90) cc_final: 0.7577 (mtm180) REVERT: A 1017 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8878 (pt) REVERT: A 1241 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8400 (m-30) REVERT: A 1271 ARG cc_start: 0.7071 (ttt180) cc_final: 0.6609 (mtm110) REVERT: A 1558 ARG cc_start: 0.5940 (mtp180) cc_final: 0.5459 (mtm180) REVERT: A 1590 MET cc_start: 0.9190 (mmp) cc_final: 0.8935 (mmt) REVERT: A 1612 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7653 (mtm180) REVERT: A 1712 THR cc_start: 0.8565 (p) cc_final: 0.8073 (m) outliers start: 28 outliers final: 14 residues processed: 123 average time/residue: 0.1365 time to fit residues: 24.7234 Evaluate side-chains 100 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1575 VAL Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1612 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 153 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 900 ASN A1088 GLN A1551 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.077362 restraints weight = 23482.875| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.75 r_work: 0.2712 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 14987 Z= 0.265 Angle : 0.720 11.549 20490 Z= 0.367 Chirality : 0.050 0.238 2236 Planarity : 0.006 0.067 2628 Dihedral : 6.231 57.774 2448 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.00 % Allowed : 10.59 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.19), residues: 1769 helix: 0.95 (0.28), residues: 369 sheet: 0.25 (0.25), residues: 443 loop : -1.27 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 255 TYR 0.020 0.002 TYR A1461 PHE 0.024 0.003 PHE A1019 TRP 0.016 0.002 TRP A1360 HIS 0.007 0.002 HIS A 678 Details of bonding type rmsd covalent geometry : bond 0.00651 (14958) covalent geometry : angle 0.70447 (20408) SS BOND : bond 0.00559 ( 5) SS BOND : angle 2.01410 ( 10) hydrogen bonds : bond 0.06224 ( 522) hydrogen bonds : angle 5.47303 ( 1446) link_BETA1-4 : bond 0.00924 ( 11) link_BETA1-4 : angle 3.11516 ( 33) link_BETA1-6 : bond 0.00221 ( 1) link_BETA1-6 : angle 1.14195 ( 3) link_NAG-ASN : bond 0.00537 ( 12) link_NAG-ASN : angle 1.91470 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 57 CYS cc_start: 0.8237 (OUTLIER) cc_final: 0.8001 (m) REVERT: A 159 GLN cc_start: 0.6836 (mm-40) cc_final: 0.6352 (mp-120) REVERT: A 334 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8558 (pp) REVERT: A 387 ARG cc_start: 0.8226 (mpt-90) cc_final: 0.7644 (mtm180) REVERT: A 898 ASP cc_start: 0.7824 (t70) cc_final: 0.7276 (t0) REVERT: A 1017 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8922 (pt) REVERT: A 1558 ARG cc_start: 0.6030 (mtp180) cc_final: 0.5450 (mtm180) REVERT: A 1612 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7769 (mtm180) REVERT: A 1712 THR cc_start: 0.8675 (p) cc_final: 0.8203 (m) outliers start: 31 outliers final: 15 residues processed: 111 average time/residue: 0.1346 time to fit residues: 22.5552 Evaluate side-chains 103 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1612 ARG Chi-restraints excluded: chain A residue 1821 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 11 optimal weight: 0.0060 chunk 146 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 135 optimal weight: 0.0270 overall best weight: 0.9458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1551 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.081570 restraints weight = 23309.158| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.69 r_work: 0.2784 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14987 Z= 0.105 Angle : 0.567 10.883 20490 Z= 0.286 Chirality : 0.044 0.209 2236 Planarity : 0.004 0.066 2628 Dihedral : 5.629 55.692 2448 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.23 % Allowed : 11.56 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1769 helix: 1.31 (0.28), residues: 370 sheet: 0.42 (0.26), residues: 424 loop : -1.09 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 524 TYR 0.012 0.001 TYR A1461 PHE 0.021 0.001 PHE A1792 TRP 0.013 0.001 TRP A1322 HIS 0.004 0.001 HIS A 550 Details of bonding type rmsd covalent geometry : bond 0.00225 (14958) covalent geometry : angle 0.55027 (20408) SS BOND : bond 0.00322 ( 5) SS BOND : angle 1.88180 ( 10) hydrogen bonds : bond 0.04184 ( 522) hydrogen bonds : angle 5.08067 ( 1446) link_BETA1-4 : bond 0.00919 ( 11) link_BETA1-4 : angle 2.84240 ( 33) link_BETA1-6 : bond 0.00385 ( 1) link_BETA1-6 : angle 0.93019 ( 3) link_NAG-ASN : bond 0.00417 ( 12) link_NAG-ASN : angle 1.61369 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 111 LEU cc_start: 0.8017 (mp) cc_final: 0.7814 (mp) REVERT: A 159 GLN cc_start: 0.6797 (mm-40) cc_final: 0.6297 (mp-120) REVERT: A 387 ARG cc_start: 0.8210 (mpt-90) cc_final: 0.7523 (mtm180) REVERT: A 993 TYR cc_start: 0.8159 (m-80) cc_final: 0.7910 (m-80) REVERT: A 1558 ARG cc_start: 0.5929 (mtp180) cc_final: 0.5442 (mtm180) REVERT: A 1612 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7894 (mtp85) REVERT: A 1712 THR cc_start: 0.8630 (p) cc_final: 0.8125 (m) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 0.1291 time to fit residues: 20.1720 Evaluate side-chains 95 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1575 VAL Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1612 ARG Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1821 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.099360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.080032 restraints weight = 23453.840| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.65 r_work: 0.2750 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14987 Z= 0.161 Angle : 0.606 10.817 20490 Z= 0.308 Chirality : 0.046 0.219 2236 Planarity : 0.005 0.066 2628 Dihedral : 5.788 56.236 2448 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.74 % Allowed : 11.04 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1769 helix: 1.30 (0.28), residues: 367 sheet: 0.38 (0.26), residues: 430 loop : -1.13 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 524 TYR 0.016 0.001 TYR A1461 PHE 0.022 0.002 PHE A1792 TRP 0.013 0.001 TRP A1360 HIS 0.004 0.001 HIS A 678 Details of bonding type rmsd covalent geometry : bond 0.00388 (14958) covalent geometry : angle 0.59161 (20408) SS BOND : bond 0.00215 ( 5) SS BOND : angle 1.58781 ( 10) hydrogen bonds : bond 0.04958 ( 522) hydrogen bonds : angle 5.13460 ( 1446) link_BETA1-4 : bond 0.00869 ( 11) link_BETA1-4 : angle 2.86421 ( 33) link_BETA1-6 : bond 0.00327 ( 1) link_BETA1-6 : angle 1.06210 ( 3) link_NAG-ASN : bond 0.00426 ( 12) link_NAG-ASN : angle 1.56813 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 57 CYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7783 (m) REVERT: A 159 GLN cc_start: 0.6831 (mm-40) cc_final: 0.6397 (mp-120) REVERT: A 242 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7933 (ttm170) REVERT: A 387 ARG cc_start: 0.8168 (mpt-90) cc_final: 0.7537 (mtm180) REVERT: A 898 ASP cc_start: 0.7761 (t70) cc_final: 0.7252 (t0) REVERT: A 993 TYR cc_start: 0.8168 (m-80) cc_final: 0.7944 (m-80) REVERT: A 1017 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8888 (pt) REVERT: A 1241 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8419 (m-30) REVERT: A 1558 ARG cc_start: 0.5930 (mtp180) cc_final: 0.5453 (mtm180) REVERT: A 1612 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7995 (mtp85) REVERT: A 1712 THR cc_start: 0.8656 (p) cc_final: 0.8158 (m) outliers start: 27 outliers final: 16 residues processed: 103 average time/residue: 0.1250 time to fit residues: 19.7734 Evaluate side-chains 100 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1575 VAL Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1612 ARG Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1821 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 63 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1551 HIS A1748 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.079015 restraints weight = 23430.983| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.67 r_work: 0.2738 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14987 Z= 0.194 Angle : 0.638 11.270 20490 Z= 0.325 Chirality : 0.048 0.222 2236 Planarity : 0.005 0.068 2628 Dihedral : 6.015 56.801 2448 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.19 % Allowed : 11.04 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.20), residues: 1769 helix: 1.19 (0.28), residues: 366 sheet: 0.35 (0.26), residues: 427 loop : -1.19 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.017 0.002 TYR A1461 PHE 0.024 0.002 PHE A1792 TRP 0.014 0.001 TRP A1360 HIS 0.005 0.001 HIS A 678 Details of bonding type rmsd covalent geometry : bond 0.00474 (14958) covalent geometry : angle 0.62349 (20408) SS BOND : bond 0.00244 ( 5) SS BOND : angle 1.83855 ( 10) hydrogen bonds : bond 0.05400 ( 522) hydrogen bonds : angle 5.22779 ( 1446) link_BETA1-4 : bond 0.00864 ( 11) link_BETA1-4 : angle 2.90950 ( 33) link_BETA1-6 : bond 0.00379 ( 1) link_BETA1-6 : angle 1.01126 ( 3) link_NAG-ASN : bond 0.00468 ( 12) link_NAG-ASN : angle 1.58010 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 57 CYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7957 (m) REVERT: A 159 GLN cc_start: 0.6825 (mm-40) cc_final: 0.6363 (mp-120) REVERT: A 242 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7938 (ttm170) REVERT: A 387 ARG cc_start: 0.8113 (mpt-90) cc_final: 0.7439 (mtm180) REVERT: A 443 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.7995 (pp) REVERT: A 898 ASP cc_start: 0.7878 (t70) cc_final: 0.7394 (t0) REVERT: A 993 TYR cc_start: 0.8175 (m-80) cc_final: 0.7948 (m-80) REVERT: A 1017 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8880 (pt) REVERT: A 1241 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8449 (m-30) REVERT: A 1429 LEU cc_start: 0.8792 (mt) cc_final: 0.8574 (mp) REVERT: A 1558 ARG cc_start: 0.6025 (mtp180) cc_final: 0.5521 (mtm180) REVERT: A 1612 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7644 (mtm180) REVERT: A 1712 THR cc_start: 0.8601 (p) cc_final: 0.8072 (m) outliers start: 34 outliers final: 19 residues processed: 108 average time/residue: 0.1259 time to fit residues: 20.7914 Evaluate side-chains 107 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1575 VAL Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1612 ARG Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1821 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 20 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 92 optimal weight: 0.0470 chunk 88 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1551 HIS A1748 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.101762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.082300 restraints weight = 23433.343| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.65 r_work: 0.2796 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14987 Z= 0.097 Angle : 0.537 10.558 20490 Z= 0.271 Chirality : 0.044 0.204 2236 Planarity : 0.004 0.065 2628 Dihedral : 5.468 55.224 2448 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.23 % Allowed : 12.33 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1769 helix: 1.48 (0.28), residues: 367 sheet: 0.50 (0.26), residues: 421 loop : -1.05 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 524 TYR 0.011 0.001 TYR A1461 PHE 0.024 0.001 PHE A1792 TRP 0.012 0.001 TRP A1360 HIS 0.003 0.001 HIS A 550 Details of bonding type rmsd covalent geometry : bond 0.00213 (14958) covalent geometry : angle 0.52278 (20408) SS BOND : bond 0.00079 ( 5) SS BOND : angle 1.12994 ( 10) hydrogen bonds : bond 0.03750 ( 522) hydrogen bonds : angle 4.89617 ( 1446) link_BETA1-4 : bond 0.00819 ( 11) link_BETA1-4 : angle 2.67012 ( 33) link_BETA1-6 : bond 0.00482 ( 1) link_BETA1-6 : angle 0.99945 ( 3) link_NAG-ASN : bond 0.00362 ( 12) link_NAG-ASN : angle 1.39995 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.6789 (mm-40) cc_final: 0.6323 (mp-120) REVERT: A 387 ARG cc_start: 0.8133 (mpt-90) cc_final: 0.7397 (mtm180) REVERT: A 443 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.7933 (pp) REVERT: A 524 ARG cc_start: 0.7483 (ttp80) cc_final: 0.7145 (ttp80) REVERT: A 898 ASP cc_start: 0.7749 (t70) cc_final: 0.7273 (t0) REVERT: A 974 ASP cc_start: 0.7752 (m-30) cc_final: 0.7150 (t0) REVERT: A 993 TYR cc_start: 0.8194 (m-80) cc_final: 0.7944 (m-80) REVERT: A 1017 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8851 (pt) REVERT: A 1373 GLN cc_start: 0.6589 (mm-40) cc_final: 0.6335 (mm-40) REVERT: A 1558 ARG cc_start: 0.5837 (mtp180) cc_final: 0.5418 (mtm180) REVERT: A 1612 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7836 (mtp85) REVERT: A 1712 THR cc_start: 0.8580 (p) cc_final: 0.8088 (m) outliers start: 19 outliers final: 15 residues processed: 99 average time/residue: 0.1235 time to fit residues: 18.9462 Evaluate side-chains 99 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1575 VAL Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1612 ARG Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1821 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 17 optimal weight: 0.6980 chunk 175 optimal weight: 0.0470 chunk 150 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1748 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.083276 restraints weight = 23620.942| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.73 r_work: 0.2827 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14987 Z= 0.089 Angle : 0.510 9.731 20490 Z= 0.255 Chirality : 0.043 0.212 2236 Planarity : 0.004 0.061 2628 Dihedral : 5.091 55.986 2448 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.42 % Allowed : 12.27 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1769 helix: 1.67 (0.28), residues: 373 sheet: 0.57 (0.26), residues: 427 loop : -0.95 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 524 TYR 0.010 0.001 TYR A 98 PHE 0.025 0.001 PHE A1792 TRP 0.010 0.001 TRP A 592 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00195 (14958) covalent geometry : angle 0.49742 (20408) SS BOND : bond 0.00113 ( 5) SS BOND : angle 0.87800 ( 10) hydrogen bonds : bond 0.03324 ( 522) hydrogen bonds : angle 4.63829 ( 1446) link_BETA1-4 : bond 0.00792 ( 11) link_BETA1-4 : angle 2.52481 ( 33) link_BETA1-6 : bond 0.00448 ( 1) link_BETA1-6 : angle 1.10770 ( 3) link_NAG-ASN : bond 0.00283 ( 12) link_NAG-ASN : angle 1.28405 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.6766 (mm-40) cc_final: 0.6331 (mp-120) REVERT: A 387 ARG cc_start: 0.8081 (mpt-90) cc_final: 0.7324 (mtm180) REVERT: A 443 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.7913 (pp) REVERT: A 524 ARG cc_start: 0.7515 (ttp80) cc_final: 0.7220 (ttp80) REVERT: A 974 ASP cc_start: 0.7651 (m-30) cc_final: 0.7006 (t0) REVERT: A 1017 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8831 (pt) REVERT: A 1233 MET cc_start: 0.8597 (mmm) cc_final: 0.8384 (mmt) REVERT: A 1373 GLN cc_start: 0.6648 (mm-40) cc_final: 0.6420 (mm110) REVERT: A 1558 ARG cc_start: 0.5918 (mtp180) cc_final: 0.5460 (mtm180) REVERT: A 1612 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7734 (mtp85) REVERT: A 1712 THR cc_start: 0.8447 (p) cc_final: 0.8007 (m) outliers start: 22 outliers final: 12 residues processed: 115 average time/residue: 0.1240 time to fit residues: 21.9633 Evaluate side-chains 96 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1575 VAL Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1612 ARG Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1821 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 155 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1748 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.078837 restraints weight = 23628.889| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.78 r_work: 0.2749 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14987 Z= 0.165 Angle : 0.601 10.464 20490 Z= 0.306 Chirality : 0.047 0.222 2236 Planarity : 0.005 0.066 2628 Dihedral : 5.554 56.237 2448 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.03 % Allowed : 12.65 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.20), residues: 1769 helix: 1.45 (0.28), residues: 373 sheet: 0.53 (0.26), residues: 432 loop : -1.03 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.015 0.002 TYR A1172 PHE 0.022 0.002 PHE A1019 TRP 0.014 0.001 TRP A1322 HIS 0.005 0.001 HIS A 678 Details of bonding type rmsd covalent geometry : bond 0.00400 (14958) covalent geometry : angle 0.58872 (20408) SS BOND : bond 0.00195 ( 5) SS BOND : angle 1.52110 ( 10) hydrogen bonds : bond 0.04814 ( 522) hydrogen bonds : angle 4.96947 ( 1446) link_BETA1-4 : bond 0.00767 ( 11) link_BETA1-4 : angle 2.64678 ( 33) link_BETA1-6 : bond 0.00342 ( 1) link_BETA1-6 : angle 1.13360 ( 3) link_NAG-ASN : bond 0.00384 ( 12) link_NAG-ASN : angle 1.37291 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.6744 (mm-40) cc_final: 0.6281 (mp-120) REVERT: A 387 ARG cc_start: 0.8060 (mpt-90) cc_final: 0.7327 (mtm180) REVERT: A 443 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.7960 (pp) REVERT: A 898 ASP cc_start: 0.7735 (t70) cc_final: 0.7280 (t0) REVERT: A 974 ASP cc_start: 0.7744 (m-30) cc_final: 0.7143 (t0) REVERT: A 1017 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8876 (pt) REVERT: A 1373 GLN cc_start: 0.6616 (mm-40) cc_final: 0.6369 (mm-40) REVERT: A 1558 ARG cc_start: 0.5895 (mtp180) cc_final: 0.5414 (mtm180) REVERT: A 1612 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8006 (mtp85) REVERT: A 1712 THR cc_start: 0.8545 (p) cc_final: 0.8084 (m) outliers start: 16 outliers final: 12 residues processed: 94 average time/residue: 0.1270 time to fit residues: 18.5315 Evaluate side-chains 93 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1575 VAL Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1612 ARG Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1821 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 168 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1551 HIS A1746 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.078117 restraints weight = 23716.885| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.81 r_work: 0.2736 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14987 Z= 0.192 Angle : 0.629 11.056 20490 Z= 0.321 Chirality : 0.047 0.224 2236 Planarity : 0.005 0.070 2628 Dihedral : 5.821 56.626 2448 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.16 % Allowed : 12.33 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1769 helix: 1.33 (0.28), residues: 367 sheet: 0.51 (0.26), residues: 426 loop : -1.08 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 524 TYR 0.015 0.002 TYR A1172 PHE 0.030 0.002 PHE A1792 TRP 0.012 0.001 TRP A1360 HIS 0.005 0.001 HIS A 678 Details of bonding type rmsd covalent geometry : bond 0.00466 (14958) covalent geometry : angle 0.61600 (20408) SS BOND : bond 0.00234 ( 5) SS BOND : angle 1.58219 ( 10) hydrogen bonds : bond 0.05231 ( 522) hydrogen bonds : angle 5.11506 ( 1446) link_BETA1-4 : bond 0.00812 ( 11) link_BETA1-4 : angle 2.73971 ( 33) link_BETA1-6 : bond 0.00356 ( 1) link_BETA1-6 : angle 1.05018 ( 3) link_NAG-ASN : bond 0.00436 ( 12) link_NAG-ASN : angle 1.47798 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3581.61 seconds wall clock time: 62 minutes 21.51 seconds (3741.51 seconds total)