Starting phenix.real_space_refine on Sun Feb 8 10:12:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3u_25671/02_2026/7t3u_25671.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3u_25671/02_2026/7t3u_25671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t3u_25671/02_2026/7t3u_25671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3u_25671/02_2026/7t3u_25671.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t3u_25671/02_2026/7t3u_25671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3u_25671/02_2026/7t3u_25671.map" } resolution = 3.7 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 18 5.49 5 S 119 5.16 5 C 27584 2.51 5 N 8231 2.21 5 O 8541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44501 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 12132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2020, 12132 Classifications: {'peptide': 2020} Incomplete info: {'truncation_to_alanine': 1232} Link IDs: {'PTRANS': 56, 'TRANS': 1963} Chain breaks: 27 Unresolved chain link angles: 40 Unresolved non-hydrogen bonds: 4452 Unresolved non-hydrogen angles: 5693 Unresolved non-hydrogen dihedrals: 3672 Unresolved non-hydrogen chiralities: 423 Planarities with less than four sites: {'PHE:plan': 60, 'HIS:plan': 47, 'ASP:plan': 77, 'TYR:plan': 41, 'GLU:plan': 94, 'ASN:plan1': 73, 'ARG:plan': 64, 'GLN:plan1': 73, 'TRP:plan': 12} Unresolved non-hydrogen planarities: 2428 Chain: "B" Number of atoms: 10375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1662, 10375 Classifications: {'peptide': 1662} Incomplete info: {'truncation_to_alanine': 914} Link IDs: {'PTRANS': 41, 'TRANS': 1620} Chain breaks: 23 Unresolved chain link angles: 24 Unresolved non-hydrogen bonds: 3327 Unresolved non-hydrogen angles: 4248 Unresolved non-hydrogen dihedrals: 2736 Unresolved non-hydrogen chiralities: 318 Planarities with less than four sites: {'GLU:plan': 76, 'ARG:plan': 50, 'ASP:plan': 58, 'PHE:plan': 46, 'ASN:plan1': 45, 'GLN:plan1': 56, 'TYR:plan': 32, 'HIS:plan': 38, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 1831 Chain: "C" Number of atoms: 9741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1575, 9741 Classifications: {'peptide': 1575} Incomplete info: {'truncation_to_alanine': 889} Link IDs: {'PTRANS': 40, 'TRANS': 1534} Chain breaks: 19 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 3242 Unresolved non-hydrogen angles: 4121 Unresolved non-hydrogen dihedrals: 2665 Unresolved non-hydrogen chiralities: 299 Planarities with less than four sites: {'GLU:plan': 73, 'ARG:plan': 51, 'ASP:plan': 60, 'PHE:plan': 44, 'ASN:plan1': 47, 'GLN:plan1': 55, 'TYR:plan': 29, 'HIS:plan': 38, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 1781 Chain: "D" Number of atoms: 12073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2012, 12073 Classifications: {'peptide': 2012} Incomplete info: {'truncation_to_alanine': 1230} Link IDs: {'PTRANS': 56, 'TRANS': 1955} Chain breaks: 27 Unresolved chain link angles: 40 Unresolved non-hydrogen bonds: 4446 Unresolved non-hydrogen angles: 5685 Unresolved non-hydrogen dihedrals: 3668 Unresolved non-hydrogen chiralities: 422 Planarities with less than four sites: {'PHE:plan': 60, 'HIS:plan': 47, 'ASP:plan': 77, 'TYR:plan': 41, 'GLU:plan': 94, 'ASN:plan1': 72, 'ARG:plan': 64, 'GLN:plan1': 73, 'TRP:plan': 12} Unresolved non-hydrogen planarities: 2425 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11509 SG CYS A2538 110.486 132.912 90.143 1.00 61.07 S ATOM 11534 SG CYS A2541 111.392 130.302 87.522 1.00 56.20 S ATOM 21884 SG CYS B2538 121.500 106.522 89.963 1.00 41.02 S ATOM 21909 SG CYS B2541 124.217 107.618 87.436 1.00 40.94 S ATOM 31625 SG CYS C2538 147.600 117.341 89.938 1.00 52.35 S ATOM 31650 SG CYS C2541 146.663 120.200 87.489 1.00 58.20 S ATOM 43698 SG CYS D2538 136.800 143.535 89.954 1.00 65.83 S ATOM 43723 SG CYS D2541 133.997 142.564 87.449 1.00 57.15 S Time building chain proxies: 10.91, per 1000 atoms: 0.25 Number of scatterers: 44501 At special positions: 0 Unit cell: (258.336, 255.852, 173.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 119 16.00 P 18 15.00 O 8541 8.00 N 8231 7.00 C 27584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2455 " - pdb=" SG CYS A2461 " distance=2.03 Simple disulfide: pdb=" SG CYS B2455 " - pdb=" SG CYS B2461 " distance=2.03 Simple disulfide: pdb=" SG CYS C2455 " - pdb=" SG CYS C2461 " distance=2.03 Simple disulfide: pdb=" SG CYS D2455 " - pdb=" SG CYS D2461 " 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 Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2701 " pdb="ZN ZN A2701 " - pdb=" NE2 HIS A2558 " pdb="ZN ZN A2701 " - pdb=" ND1 HIS A2563 " pdb="ZN ZN A2701 " - pdb=" SG CYS A2541 " pdb="ZN ZN A2701 " - pdb=" SG CYS A2538 " pdb=" ZN B2701 " pdb="ZN ZN B2701 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B2701 " - pdb=" ND1 HIS B2563 " pdb="ZN ZN B2701 " - pdb=" SG CYS B2541 " pdb="ZN ZN B2701 " - pdb=" SG CYS B2538 " pdb=" ZN C2701 " pdb="ZN ZN C2701 " - pdb=" NE2 HIS C2558 " pdb="ZN ZN C2701 " - pdb=" ND1 HIS C2563 " pdb="ZN ZN C2701 " - pdb=" SG CYS C2541 " pdb="ZN ZN C2701 " - pdb=" SG CYS C2538 " pdb=" ZN D2701 " pdb="ZN ZN D2701 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D2701 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D2701 " - pdb=" SG CYS D2541 " pdb="ZN ZN D2701 " - pdb=" SG CYS D2538 " Number of angles added : 4 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14000 Finding SS restraints... Secondary structure from input PDB file: 385 helices and 29 sheets defined 71.6% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 87 through 111 Processing helix chain 'A' and resid 435 through 462 Processing helix chain 'A' and resid 465 through 485 Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.987A pdb=" N ILE A 496 " --> pdb=" O VAL A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 513 through 527 Proline residue: A 525 - end of helix Processing helix chain 'A' and resid 546 through 563 Processing helix chain 'A' and resid 567 through 577 removed outlier: 4.245A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 584 Processing helix chain 'A' and resid 591 through 599 Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 611 through 626 Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.884A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 637 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS A 638 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 658 removed outlier: 3.781A pdb=" N ASP A 658 " --> pdb=" O LYS A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 718 Processing helix chain 'A' and resid 719 through 740 Processing helix chain 'A' and resid 744 through 755 removed outlier: 4.807A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 765 Processing helix chain 'A' and resid 770 through 786 removed outlier: 3.535A pdb=" N VAL A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 818 Processing helix chain 'A' and resid 830 through 846 Processing helix chain 'A' and resid 853 through 873 removed outlier: 3.676A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 891 removed outlier: 3.943A pdb=" N ARG A 883 " --> pdb=" O SER A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 998 Processing helix chain 'A' and resid 1026 through 1036 Processing helix chain 'A' and resid 1052 through 1064 Processing helix chain 'A' and resid 1067 through 1082 removed outlier: 3.832A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1093 removed outlier: 3.666A pdb=" N GLU A1087 " --> pdb=" O SER A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1123 removed outlier: 3.924A pdb=" N TYR A1107 " --> pdb=" O ASP A1103 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A1108 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A1116 " --> pdb=" O SER A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1183 Processing helix chain 'A' and resid 1189 through 1201 Processing helix chain 'A' and resid 1201 through 1212 removed outlier: 4.077A pdb=" N VAL A1205 " --> pdb=" O ASP A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1235 Processing helix chain 'A' and resid 1239 through 1249 removed outlier: 3.852A pdb=" N HIS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1254 Processing helix chain 'A' and resid 1257 through 1268 removed outlier: 3.765A pdb=" N PHE A1268 " --> pdb=" O MET A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1277 Processing helix chain 'A' and resid 1279 through 1294 removed outlier: 3.778A pdb=" N LEU A1283 " --> pdb=" O SER A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1308 removed outlier: 3.612A pdb=" N LEU A1300 " --> pdb=" O HIS A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1329 Processing helix chain 'A' and resid 1338 through 1352 Processing helix chain 'A' and resid 1360 through 1376 Processing helix chain 'A' and resid 1380 through 1391 Processing helix chain 'A' and resid 1392 through 1401 removed outlier: 3.511A pdb=" N VAL A1396 " --> pdb=" O PRO A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1417 Processing helix chain 'A' and resid 1439 through 1447 removed outlier: 3.973A pdb=" N ASN A1443 " --> pdb=" O THR A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1482 removed outlier: 3.659A pdb=" N SER A1470 " --> pdb=" O LYS A1466 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL A1471 " --> pdb=" O TYR A1467 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A1476 " --> pdb=" O VAL A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1496 Processing helix chain 'A' and resid 1496 through 1505 removed outlier: 5.882A pdb=" N LEU A1502 " --> pdb=" O VAL A1498 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLN A1503 " --> pdb=" O VAL A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1510 Processing helix chain 'A' and resid 1516 through 1528 Processing helix chain 'A' and resid 1590 through 1623 removed outlier: 3.739A pdb=" N LYS A1594 " --> pdb=" O ASN A1590 " (cutoff:3.500A) Proline residue: A1608 - end of helix removed outlier: 3.865A pdb=" N GLN A1611 " --> pdb=" O LYS A1607 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A1612 " --> pdb=" O PRO A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1624 through 1627 Processing helix chain 'A' and resid 1632 through 1638 Processing helix chain 'A' and resid 1641 through 1653 Processing helix chain 'A' and resid 1658 through 1673 Processing helix chain 'A' and resid 1680 through 1695 removed outlier: 3.927A pdb=" N GLN A1685 " --> pdb=" O ASP A1681 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU A1686 " --> pdb=" O ARG A1682 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1732 Processing helix chain 'A' and resid 1732 through 1742 Processing helix chain 'A' and resid 1746 through 1760 Processing helix chain 'A' and resid 1765 through 1779 Processing helix chain 'A' and resid 1781 through 1794 removed outlier: 3.505A pdb=" N LYS A1787 " --> pdb=" O GLU A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1866 through 1882 Proline residue: A1872 - end of helix Processing helix chain 'A' and resid 1885 through 1894 removed outlier: 3.556A pdb=" N GLN A1889 " --> pdb=" O ASN A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1903 through 1913 Processing helix chain 'A' and resid 1933 through 1949 removed outlier: 3.514A pdb=" N VAL A1937 " --> pdb=" O ASN A1933 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS A1948 " --> pdb=" O LEU A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1961 Processing helix chain 'A' and resid 1965 through 1976 Processing helix chain 'A' and resid 1988 through 2003 Processing helix chain 'A' and resid 2013 through 2020 removed outlier: 4.138A pdb=" N SER A2019 " --> pdb=" O ARG A2015 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A2020 " --> pdb=" O ILE A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2033 Processing helix chain 'A' and resid 2045 through 2062 removed outlier: 3.830A pdb=" N VAL A2049 " --> pdb=" O SER A2045 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2071 Processing helix chain 'A' and resid 2113 through 2119 Processing helix chain 'A' and resid 2141 through 2146 Processing helix chain 'A' and resid 2148 through 2158 Processing helix chain 'A' and resid 2167 through 2191 removed outlier: 4.077A pdb=" N ASP A2173 " --> pdb=" O SER A2169 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A2190 " --> pdb=" O ARG A2186 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET A2191 " --> pdb=" O LYS A2187 " (cutoff:3.500A) Processing helix chain 'A' and resid 2191 through 2200 removed outlier: 3.527A pdb=" N ARG A2200 " --> pdb=" O TRP A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2201 through 2222 removed outlier: 3.578A pdb=" N GLY A2205 " --> pdb=" O MET A2201 " (cutoff:3.500A) Processing helix chain 'A' and resid 2262 through 2276 Processing helix chain 'A' and resid 2279 through 2303 Processing helix chain 'A' and resid 2319 through 2336 Processing helix chain 'A' and resid 2337 through 2346 removed outlier: 3.811A pdb=" N TYR A2341 " --> pdb=" O GLU A2338 " (cutoff:3.500A) Processing helix chain 'A' and resid 2347 through 2352 Processing helix chain 'A' and resid 2353 through 2364 Processing helix chain 'A' and resid 2365 through 2390 Processing helix chain 'A' and resid 2457 through 2468 Processing helix chain 'A' and resid 2474 through 2479 removed outlier: 4.135A pdb=" N GLY A2477 " --> pdb=" O GLY A2474 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2505 Processing helix chain 'A' and resid 2507 through 2537 removed outlier: 4.336A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE A2516 " --> pdb=" O ILE A2512 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2549 removed outlier: 3.551A pdb=" N ASP A2549 " --> pdb=" O ASP A2546 " (cutoff:3.500A) Processing helix chain 'A' and resid 2554 through 2559 Processing helix chain 'A' and resid 2564 through 2576 Processing helix chain 'A' and resid 2584 through 2596 Processing helix chain 'A' and resid 2607 through 2611 Processing helix chain 'B' and resid 437 through 462 Processing helix chain 'B' and resid 465 through 485 Processing helix chain 'B' and resid 504 through 511 Processing helix chain 'B' and resid 514 through 527 Proline residue: B 525 - end of helix Processing helix chain 'B' and resid 546 through 564 Processing helix chain 'B' and resid 567 through 577 removed outlier: 3.802A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 Processing helix chain 'B' and resid 591 through 599 Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 611 through 626 Processing helix chain 'B' and resid 627 through 639 removed outlier: 3.954A pdb=" N LEU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 656 Processing helix chain 'B' and resid 658 through 662 Processing helix chain 'B' and resid 708 through 718 Processing helix chain 'B' and resid 719 through 740 removed outlier: 3.911A pdb=" N VAL B 725 " --> pdb=" O HIS B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 755 removed outlier: 3.980A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 765 Processing helix chain 'B' and resid 770 through 785 Processing helix chain 'B' and resid 813 through 819 Processing helix chain 'B' and resid 830 through 846 Processing helix chain 'B' and resid 853 through 874 Processing helix chain 'B' and resid 878 through 893 Processing helix chain 'B' and resid 962 through 997 removed outlier: 3.869A pdb=" N GLU B 997 " --> pdb=" O VAL B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1036 removed outlier: 3.912A pdb=" N ALA B1034 " --> pdb=" O GLU B1030 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N MET B1035 " --> pdb=" O GLN B1031 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1064 removed outlier: 3.899A pdb=" N LEU B1056 " --> pdb=" O GLY B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1082 removed outlier: 3.699A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1093 Processing helix chain 'B' and resid 1102 through 1123 removed outlier: 3.774A pdb=" N LYS B1123 " --> pdb=" O THR B1119 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1183 removed outlier: 3.620A pdb=" N CYS B1183 " --> pdb=" O LEU B1179 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1200 Processing helix chain 'B' and resid 1201 through 1211 removed outlier: 3.959A pdb=" N VAL B1205 " --> pdb=" O ASP B1201 " (cutoff:3.500A) Processing helix chain 'B' and resid 1218 through 1236 Processing helix chain 'B' and resid 1239 through 1249 removed outlier: 3.934A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) Processing helix chain 'B' and resid 1258 through 1268 Processing helix chain 'B' and resid 1271 through 1277 Processing helix chain 'B' and resid 1279 through 1292 removed outlier: 3.559A pdb=" N LEU B1283 " --> pdb=" O SER B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1296 through 1307 removed outlier: 3.702A pdb=" N LEU B1300 " --> pdb=" O HIS B1296 " (cutoff:3.500A) Processing helix chain 'B' and resid 1320 through 1329 Processing helix chain 'B' and resid 1330 through 1332 No H-bonds generated for 'chain 'B' and resid 1330 through 1332' Processing helix chain 'B' and resid 1340 through 1352 Processing helix chain 'B' and resid 1360 through 1378 removed outlier: 4.198A pdb=" N GLY B1378 " --> pdb=" O ALA B1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1391 Processing helix chain 'B' and resid 1392 through 1402 Processing helix chain 'B' and resid 1406 through 1421 Processing helix chain 'B' and resid 1429 through 1434 removed outlier: 3.996A pdb=" N THR B1433 " --> pdb=" O GLU B1430 " (cutoff:3.500A) Processing helix chain 'B' and resid 1435 through 1453 removed outlier: 3.983A pdb=" N ALA B1449 " --> pdb=" O THR B1445 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG B1450 " --> pdb=" O LEU B1446 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B1451 " --> pdb=" O ASP B1447 " (cutoff:3.500A) Processing helix chain 'B' and resid 1462 through 1471 Processing helix chain 'B' and resid 1471 through 1480 Processing helix chain 'B' and resid 1492 through 1510 removed outlier: 3.931A pdb=" N ILE B1497 " --> pdb=" O THR B1493 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL B1498 " --> pdb=" O HIS B1494 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG B1507 " --> pdb=" O GLN B1503 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B1508 " --> pdb=" O SER B1504 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B1509 " --> pdb=" O THR B1505 " (cutoff:3.500A) Processing helix chain 'B' and resid 1517 through 1520 Processing helix chain 'B' and resid 1521 through 1530 removed outlier: 4.091A pdb=" N CYS B1525 " --> pdb=" O SER B1521 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B1526 " --> pdb=" O VAL B1522 " (cutoff:3.500A) Processing helix chain 'B' and resid 1590 through 1623 Proline residue: B1608 - end of helix removed outlier: 3.778A pdb=" N GLN B1611 " --> pdb=" O LYS B1607 " (cutoff:3.500A) Processing helix chain 'B' and resid 1624 through 1627 Processing helix chain 'B' and resid 1632 through 1640 Processing helix chain 'B' and resid 1641 through 1653 Processing helix chain 'B' and resid 1658 through 1673 Processing helix chain 'B' and resid 1679 through 1695 Processing helix chain 'B' and resid 1720 through 1731 Processing helix chain 'B' and resid 1732 through 1744 removed outlier: 3.829A pdb=" N LEU B1736 " --> pdb=" O GLY B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1746 through 1762 Processing helix chain 'B' and resid 1765 through 1776 removed outlier: 3.651A pdb=" N MET B1776 " --> pdb=" O PHE B1772 " (cutoff:3.500A) Processing helix chain 'B' and resid 1786 through 1800 removed outlier: 3.784A pdb=" N ARG B1792 " --> pdb=" O VAL B1788 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B1796 " --> pdb=" O ARG B1792 " (cutoff:3.500A) Processing helix chain 'B' and resid 1866 through 1882 Proline residue: B1872 - end of helix removed outlier: 3.520A pdb=" N CYS B1881 " --> pdb=" O LEU B1877 " (cutoff:3.500A) Processing helix chain 'B' and resid 1885 through 1892 Processing helix chain 'B' and resid 1903 through 1916 Processing helix chain 'B' and resid 1933 through 1949 removed outlier: 3.646A pdb=" N VAL B1937 " --> pdb=" O ASN B1933 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1961 Processing helix chain 'B' and resid 1965 through 1976 removed outlier: 3.517A pdb=" N THR B1971 " --> pdb=" O ILE B1967 " (cutoff:3.500A) Processing helix chain 'B' and resid 1978 through 1985 removed outlier: 3.713A pdb=" N LYS B1983 " --> pdb=" O SER B1979 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1986 through 2003 Processing helix chain 'B' and resid 2010 through 2020 removed outlier: 3.690A pdb=" N SER B2019 " --> pdb=" O ARG B2015 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2032 Processing helix chain 'B' and resid 2045 through 2062 removed outlier: 3.763A pdb=" N VAL B2049 " --> pdb=" O SER B2045 " (cutoff:3.500A) Processing helix chain 'B' and resid 2065 through 2071 Processing helix chain 'B' and resid 2113 through 2119 Processing helix chain 'B' and resid 2141 through 2146 Processing helix chain 'B' and resid 2148 through 2159 removed outlier: 3.619A pdb=" N THR B2159 " --> pdb=" O LEU B2155 " (cutoff:3.500A) Processing helix chain 'B' and resid 2167 through 2191 removed outlier: 3.990A pdb=" N ASP B2173 " --> pdb=" O SER B2169 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B2190 " --> pdb=" O ARG B2186 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET B2191 " --> pdb=" O LYS B2187 " (cutoff:3.500A) Processing helix chain 'B' and resid 2191 through 2200 removed outlier: 3.525A pdb=" N ARG B2200 " --> pdb=" O TRP B2196 " (cutoff:3.500A) Processing helix chain 'B' and resid 2201 through 2222 Processing helix chain 'B' and resid 2262 through 2276 Processing helix chain 'B' and resid 2279 through 2303 Processing helix chain 'B' and resid 2319 through 2336 Processing helix chain 'B' and resid 2337 through 2346 removed outlier: 3.832A pdb=" N TYR B2341 " --> pdb=" O GLU B2338 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B2342 " --> pdb=" O LEU B2339 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B2343 " --> pdb=" O PHE B2340 " (cutoff:3.500A) Processing helix chain 'B' and resid 2347 through 2352 Processing helix chain 'B' and resid 2352 through 2365 removed outlier: 3.640A pdb=" N PHE B2356 " --> pdb=" O GLU B2352 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN B2365 " --> pdb=" O SER B2361 " (cutoff:3.500A) Processing helix chain 'B' and resid 2365 through 2391 Processing helix chain 'B' and resid 2457 through 2468 Processing helix chain 'B' and resid 2474 through 2479 removed outlier: 4.156A pdb=" N GLY B2477 " --> pdb=" O GLY B2474 " (cutoff:3.500A) Processing helix chain 'B' and resid 2489 through 2505 Processing helix chain 'B' and resid 2510 through 2537 removed outlier: 4.064A pdb=" N ILE B2516 " --> pdb=" O ILE B2512 " (cutoff:3.500A) Processing helix chain 'B' and resid 2545 through 2549 removed outlier: 3.530A pdb=" N PHE B2548 " --> pdb=" O ARG B2545 " (cutoff:3.500A) Processing helix chain 'B' and resid 2554 through 2559 Processing helix chain 'B' and resid 2564 through 2576 Processing helix chain 'B' and resid 2579 through 2583 removed outlier: 3.659A pdb=" N TYR B2583 " --> pdb=" O LYS B2580 " (cutoff:3.500A) Processing helix chain 'B' and resid 2584 through 2596 Processing helix chain 'C' and resid 438 through 462 removed outlier: 4.067A pdb=" N LEU C 442 " --> pdb=" O GLU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 485 Processing helix chain 'C' and resid 502 through 512 Processing helix chain 'C' and resid 513 through 527 Proline residue: C 525 - end of helix Processing helix chain 'C' and resid 546 through 564 Processing helix chain 'C' and resid 567 through 576 Processing helix chain 'C' and resid 578 through 584 Processing helix chain 'C' and resid 590 through 599 Processing helix chain 'C' and resid 604 through 610 removed outlier: 3.687A pdb=" N LYS C 608 " --> pdb=" O LYS C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 626 Processing helix chain 'C' and resid 627 through 639 removed outlier: 3.712A pdb=" N LEU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 658 Processing helix chain 'C' and resid 708 through 718 Processing helix chain 'C' and resid 719 through 741 removed outlier: 3.512A pdb=" N ASN C 724 " --> pdb=" O ALA C 720 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 725 " --> pdb=" O HIS C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 755 Processing helix chain 'C' and resid 756 through 765 removed outlier: 3.943A pdb=" N ALA C 765 " --> pdb=" O PHE C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 784 Processing helix chain 'C' and resid 811 through 817 removed outlier: 3.563A pdb=" N TYR C 815 " --> pdb=" O ILE C 812 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP C 816 " --> pdb=" O LYS C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 846 Processing helix chain 'C' and resid 853 through 873 Processing helix chain 'C' and resid 877 through 893 Processing helix chain 'C' and resid 962 through 996 removed outlier: 3.570A pdb=" N GLU C 966 " --> pdb=" O ILE C 962 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 993 " --> pdb=" O TYR C 989 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C 994 " --> pdb=" O LEU C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1026 through 1037 removed outlier: 3.583A pdb=" N GLY C1037 " --> pdb=" O GLU C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1064 Processing helix chain 'C' and resid 1067 through 1082 Processing helix chain 'C' and resid 1083 through 1095 Processing helix chain 'C' and resid 1101 through 1123 removed outlier: 3.828A pdb=" N GLU C1105 " --> pdb=" O ALA C1101 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS C1123 " --> pdb=" O THR C1119 " (cutoff:3.500A) Processing helix chain 'C' and resid 1169 through 1183 removed outlier: 3.516A pdb=" N CYS C1183 " --> pdb=" O LEU C1179 " (cutoff:3.500A) Processing helix chain 'C' and resid 1189 through 1201 Processing helix chain 'C' and resid 1201 through 1212 removed outlier: 4.039A pdb=" N VAL C1205 " --> pdb=" O ASP C1201 " (cutoff:3.500A) Processing helix chain 'C' and resid 1218 through 1236 Processing helix chain 'C' and resid 1239 through 1249 removed outlier: 3.726A pdb=" N GLN C1243 " --> pdb=" O ASN C1239 " (cutoff:3.500A) Processing helix chain 'C' and resid 1257 through 1268 removed outlier: 4.196A pdb=" N GLU C1262 " --> pdb=" O LEU C1258 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C1268 " --> pdb=" O MET C1264 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1276 Processing helix chain 'C' and resid 1279 through 1294 removed outlier: 3.700A pdb=" N LEU C1283 " --> pdb=" O SER C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1296 through 1305 removed outlier: 3.703A pdb=" N LEU C1300 " --> pdb=" O HIS C1296 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 5.813A pdb=" N ASP C1330 " --> pdb=" O THR C1326 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASP C1331 " --> pdb=" O ASN C1327 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C1332 " --> pdb=" O ALA C1328 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1351 Processing helix chain 'C' and resid 1360 through 1377 Processing helix chain 'C' and resid 1380 through 1391 Processing helix chain 'C' and resid 1392 through 1402 removed outlier: 3.714A pdb=" N HIS C1402 " --> pdb=" O SER C1398 " (cutoff:3.500A) Processing helix chain 'C' and resid 1406 through 1420 Processing helix chain 'C' and resid 1590 through 1607 removed outlier: 3.861A pdb=" N LYS C1594 " --> pdb=" O ASN C1590 " (cutoff:3.500A) Processing helix chain 'C' and resid 1608 through 1623 removed outlier: 3.958A pdb=" N LEU C1621 " --> pdb=" O LEU C1617 " (cutoff:3.500A) Processing helix chain 'C' and resid 1624 through 1628 removed outlier: 3.961A pdb=" N LEU C1627 " --> pdb=" O PRO C1624 " (cutoff:3.500A) Processing helix chain 'C' and resid 1632 through 1638 Processing helix chain 'C' and resid 1641 through 1653 Processing helix chain 'C' and resid 1658 through 1673 removed outlier: 3.535A pdb=" N CYS C1662 " --> pdb=" O GLU C1658 " (cutoff:3.500A) Processing helix chain 'C' and resid 1680 through 1695 removed outlier: 4.007A pdb=" N LEU C1686 " --> pdb=" O ARG C1682 " (cutoff:3.500A) Processing helix chain 'C' and resid 1720 through 1732 Processing helix chain 'C' and resid 1732 through 1737 Processing helix chain 'C' and resid 1738 through 1740 No H-bonds generated for 'chain 'C' and resid 1738 through 1740' Processing helix chain 'C' and resid 1752 through 1761 Processing helix chain 'C' and resid 1765 through 1779 Processing helix chain 'C' and resid 1781 through 1798 removed outlier: 4.064A pdb=" N PHE C1786 " --> pdb=" O SER C1782 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS C1787 " --> pdb=" O GLU C1783 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C1788 " --> pdb=" O ARG C1784 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C1789 " --> pdb=" O PHE C1785 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG C1795 " --> pdb=" O ASP C1791 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C1796 " --> pdb=" O ARG C1792 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN C1798 " --> pdb=" O LYS C1794 " (cutoff:3.500A) Processing helix chain 'C' and resid 1869 through 1882 removed outlier: 4.117A pdb=" N ILE C1873 " --> pdb=" O ILE C1869 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C1874 " --> pdb=" O MET C1870 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS C1881 " --> pdb=" O LEU C1877 " (cutoff:3.500A) Processing helix chain 'C' and resid 1885 through 1894 Processing helix chain 'C' and resid 1902 through 1916 removed outlier: 3.526A pdb=" N GLU C1906 " --> pdb=" O ASN C1902 " (cutoff:3.500A) Processing helix chain 'C' and resid 1933 through 1949 removed outlier: 3.923A pdb=" N CYS C1948 " --> pdb=" O LEU C1944 " (cutoff:3.500A) Processing helix chain 'C' and resid 1956 through 1961 Processing helix chain 'C' and resid 1965 through 1976 removed outlier: 3.723A pdb=" N THR C1971 " --> pdb=" O ILE C1967 " (cutoff:3.500A) Processing helix chain 'C' and resid 1978 through 1985 removed outlier: 4.090A pdb=" N LYS C1983 " --> pdb=" O SER C1979 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1986 through 2004 Processing helix chain 'C' and resid 2010 through 2020 removed outlier: 3.567A pdb=" N SER C2019 " --> pdb=" O ARG C2015 " (cutoff:3.500A) Processing helix chain 'C' and resid 2021 through 2033 Processing helix chain 'C' and resid 2045 through 2062 Processing helix chain 'C' and resid 2065 through 2071 Processing helix chain 'C' and resid 2113 through 2120 Processing helix chain 'C' and resid 2141 through 2146 Processing helix chain 'C' and resid 2148 through 2158 Processing helix chain 'C' and resid 2167 through 2191 removed outlier: 4.002A pdb=" N ASP C2173 " --> pdb=" O SER C2169 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C2190 " --> pdb=" O ARG C2186 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET C2191 " --> pdb=" O LYS C2187 " (cutoff:3.500A) Processing helix chain 'C' and resid 2191 through 2200 removed outlier: 3.589A pdb=" N ARG C2200 " --> pdb=" O TRP C2196 " (cutoff:3.500A) Processing helix chain 'C' and resid 2201 through 2222 Processing helix chain 'C' and resid 2262 through 2276 Processing helix chain 'C' and resid 2279 through 2303 Processing helix chain 'C' and resid 2319 through 2336 Processing helix chain 'C' and resid 2342 through 2346 Processing helix chain 'C' and resid 2347 through 2352 Processing helix chain 'C' and resid 2353 through 2365 removed outlier: 4.805A pdb=" N ASN C2365 " --> pdb=" O SER C2361 " (cutoff:3.500A) Processing helix chain 'C' and resid 2365 through 2390 Processing helix chain 'C' and resid 2457 through 2468 Processing helix chain 'C' and resid 2474 through 2479 removed outlier: 4.064A pdb=" N GLY C2477 " --> pdb=" O GLY C2474 " (cutoff:3.500A) Processing helix chain 'C' and resid 2489 through 2505 Processing helix chain 'C' and resid 2507 through 2537 removed outlier: 4.240A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE C2516 " --> pdb=" O ILE C2512 " (cutoff:3.500A) Processing helix chain 'C' and resid 2545 through 2549 Processing helix chain 'C' and resid 2554 through 2559 Processing helix chain 'C' and resid 2564 through 2576 removed outlier: 3.520A pdb=" N LEU C2569 " --> pdb=" O MET C2565 " (cutoff:3.500A) Processing helix chain 'C' and resid 2579 through 2583 removed outlier: 3.660A pdb=" N TYR C2583 " --> pdb=" O LYS C2580 " (cutoff:3.500A) Processing helix chain 'C' and resid 2584 through 2596 Processing helix chain 'C' and resid 2607 through 2611 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 89 through 111 Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 435 through 462 Processing helix chain 'D' and resid 465 through 485 Processing helix chain 'D' and resid 502 through 512 Processing helix chain 'D' and resid 513 through 527 Proline residue: D 525 - end of helix Processing helix chain 'D' and resid 546 through 564 Processing helix chain 'D' and resid 567 through 577 removed outlier: 4.118A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 584 removed outlier: 4.072A pdb=" N MET D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 599 Processing helix chain 'D' and resid 602 through 610 Processing helix chain 'D' and resid 611 through 626 Processing helix chain 'D' and resid 627 through 639 removed outlier: 3.636A pdb=" N VAL D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 658 Processing helix chain 'D' and resid 708 through 718 Processing helix chain 'D' and resid 719 through 741 Processing helix chain 'D' and resid 744 through 755 removed outlier: 3.655A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 765 Processing helix chain 'D' and resid 770 through 785 removed outlier: 3.526A pdb=" N HIS D 783 " --> pdb=" O HIS D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 820 removed outlier: 3.835A pdb=" N TYR D 815 " --> pdb=" O THR D 811 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP D 816 " --> pdb=" O ILE D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 846 Processing helix chain 'D' and resid 853 through 874 removed outlier: 4.144A pdb=" N LEU D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR D 860 " --> pdb=" O LYS D 856 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE D 861 " --> pdb=" O ASN D 857 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU D 862 " --> pdb=" O LYS D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 892 Processing helix chain 'D' and resid 962 through 998 removed outlier: 3.752A pdb=" N PHE D 998 " --> pdb=" O PHE D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1026 through 1036 removed outlier: 3.568A pdb=" N PHE D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1052 through 1064 Processing helix chain 'D' and resid 1067 through 1082 removed outlier: 3.831A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing helix chain 'D' and resid 1083 through 1095 Processing helix chain 'D' and resid 1101 through 1123 removed outlier: 3.507A pdb=" N LYS D1123 " --> pdb=" O THR D1119 " (cutoff:3.500A) Processing helix chain 'D' and resid 1169 through 1183 removed outlier: 3.724A pdb=" N CYS D1183 " --> pdb=" O LEU D1179 " (cutoff:3.500A) Processing helix chain 'D' and resid 1189 through 1201 Processing helix chain 'D' and resid 1201 through 1212 removed outlier: 3.937A pdb=" N VAL D1205 " --> pdb=" O ASP D1201 " (cutoff:3.500A) Processing helix chain 'D' and resid 1218 through 1236 Processing helix chain 'D' and resid 1239 through 1249 removed outlier: 3.621A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1254 Processing helix chain 'D' and resid 1257 through 1268 Processing helix chain 'D' and resid 1271 through 1277 Processing helix chain 'D' and resid 1279 through 1292 removed outlier: 3.638A pdb=" N LEU D1283 " --> pdb=" O SER D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1296 through 1308 Processing helix chain 'D' and resid 1320 through 1329 Processing helix chain 'D' and resid 1338 through 1351 Processing helix chain 'D' and resid 1360 through 1376 Processing helix chain 'D' and resid 1381 through 1391 Processing helix chain 'D' and resid 1393 through 1402 removed outlier: 3.668A pdb=" N HIS D1402 " --> pdb=" O SER D1398 " (cutoff:3.500A) Processing helix chain 'D' and resid 1406 through 1417 Processing helix chain 'D' and resid 1437 through 1446 Processing helix chain 'D' and resid 1447 through 1453 Processing helix chain 'D' and resid 1462 through 1480 removed outlier: 4.001A pdb=" N LYS D1466 " --> pdb=" O PRO D1462 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D1471 " --> pdb=" O TYR D1467 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN D1477 " --> pdb=" O LEU D1473 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA D1478 " --> pdb=" O ASP D1474 " (cutoff:3.500A) Processing helix chain 'D' and resid 1485 through 1489 removed outlier: 4.026A pdb=" N THR D1489 " --> pdb=" O GLU D1486 " (cutoff:3.500A) Processing helix chain 'D' and resid 1491 through 1496 removed outlier: 3.625A pdb=" N GLN D1495 " --> pdb=" O LEU D1491 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR D1496 " --> pdb=" O GLN D1492 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1491 through 1496' Processing helix chain 'D' and resid 1500 through 1508 removed outlier: 3.709A pdb=" N GLN D1503 " --> pdb=" O GLN D1500 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR D1505 " --> pdb=" O LEU D1502 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N THR D1506 " --> pdb=" O GLN D1503 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D1508 " --> pdb=" O THR D1505 " (cutoff:3.500A) Processing helix chain 'D' and resid 1515 through 1518 Processing helix chain 'D' and resid 1519 through 1524 removed outlier: 4.346A pdb=" N GLU D1523 " --> pdb=" O LYS D1519 " (cutoff:3.500A) Processing helix chain 'D' and resid 1527 through 1532 removed outlier: 4.104A pdb=" N MET D1531 " --> pdb=" O ARG D1527 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL D1532 " --> pdb=" O THR D1528 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1527 through 1532' Processing helix chain 'D' and resid 1590 through 1623 removed outlier: 3.941A pdb=" N LYS D1594 " --> pdb=" O ASN D1590 " (cutoff:3.500A) Proline residue: D1608 - end of helix Processing helix chain 'D' and resid 1624 through 1627 Processing helix chain 'D' and resid 1632 through 1640 removed outlier: 3.697A pdb=" N SER D1640 " --> pdb=" O GLN D1636 " (cutoff:3.500A) Processing helix chain 'D' and resid 1641 through 1653 Processing helix chain 'D' and resid 1658 through 1673 removed outlier: 3.767A pdb=" N LEU D1673 " --> pdb=" O LEU D1669 " (cutoff:3.500A) Processing helix chain 'D' and resid 1679 through 1695 Processing helix chain 'D' and resid 1720 through 1732 Processing helix chain 'D' and resid 1732 through 1744 Processing helix chain 'D' and resid 1746 through 1762 Processing helix chain 'D' and resid 1765 through 1779 Processing helix chain 'D' and resid 1781 through 1800 removed outlier: 4.738A pdb=" N LYS D1787 " --> pdb=" O GLU D1783 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D1792 " --> pdb=" O VAL D1788 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG D1795 " --> pdb=" O ASP D1791 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA D1796 " --> pdb=" O ARG D1792 " (cutoff:3.500A) Processing helix chain 'D' and resid 1866 through 1882 Proline residue: D1872 - end of helix Processing helix chain 'D' and resid 1885 through 1894 Processing helix chain 'D' and resid 1903 through 1916 Processing helix chain 'D' and resid 1933 through 1949 removed outlier: 3.588A pdb=" N THR D1940 " --> pdb=" O LEU D1936 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS D1948 " --> pdb=" O LEU D1944 " (cutoff:3.500A) Processing helix chain 'D' and resid 1956 through 1961 Processing helix chain 'D' and resid 1965 through 1975 removed outlier: 3.825A pdb=" N ILE D1974 " --> pdb=" O ILE D1970 " (cutoff:3.500A) Processing helix chain 'D' and resid 1988 through 2003 Processing helix chain 'D' and resid 2012 through 2020 removed outlier: 3.790A pdb=" N SER D2019 " --> pdb=" O ARG D2015 " (cutoff:3.500A) Processing helix chain 'D' and resid 2021 through 2033 Processing helix chain 'D' and resid 2045 through 2062 Processing helix chain 'D' and resid 2064 through 2071 removed outlier: 3.584A pdb=" N GLN D2068 " --> pdb=" O ASN D2064 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2120 Processing helix chain 'D' and resid 2141 through 2147 removed outlier: 3.810A pdb=" N LEU D2147 " --> pdb=" O CYS D2144 " (cutoff:3.500A) Processing helix chain 'D' and resid 2148 through 2158 Processing helix chain 'D' and resid 2167 through 2191 removed outlier: 3.520A pdb=" N PHE D2171 " --> pdb=" O LYS D2167 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP D2173 " --> pdb=" O SER D2169 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER D2190 " --> pdb=" O ARG D2186 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET D2191 " --> pdb=" O LYS D2187 " (cutoff:3.500A) Processing helix chain 'D' and resid 2191 through 2200 removed outlier: 3.796A pdb=" N ARG D2200 " --> pdb=" O TRP D2196 " (cutoff:3.500A) Processing helix chain 'D' and resid 2201 through 2222 Processing helix chain 'D' and resid 2262 through 2276 Processing helix chain 'D' and resid 2279 through 2303 Processing helix chain 'D' and resid 2319 through 2336 Processing helix chain 'D' and resid 2337 through 2345 removed outlier: 3.521A pdb=" N ILE D2343 " --> pdb=" O PHE D2340 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2352 removed outlier: 3.954A pdb=" N TYR D2350 " --> pdb=" O PHE D2346 " (cutoff:3.500A) Processing helix chain 'D' and resid 2352 through 2364 removed outlier: 3.618A pdb=" N PHE D2356 " --> pdb=" O GLU D2352 " (cutoff:3.500A) Processing helix chain 'D' and resid 2365 through 2391 Processing helix chain 'D' and resid 2457 through 2468 Processing helix chain 'D' and resid 2475 through 2479 Processing helix chain 'D' and resid 2489 through 2505 Processing helix chain 'D' and resid 2507 through 2537 removed outlier: 4.257A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE D2516 " --> pdb=" O ILE D2512 " (cutoff:3.500A) Processing helix chain 'D' and resid 2545 through 2549 Processing helix chain 'D' and resid 2554 through 2562 Processing helix chain 'D' and resid 2564 through 2576 Processing helix chain 'D' and resid 2579 through 2583 removed outlier: 3.806A pdb=" N TYR D2583 " --> pdb=" O LYS D2580 " (cutoff:3.500A) Processing helix chain 'D' and resid 2584 through 2596 Processing helix chain 'D' and resid 2607 through 2611 removed outlier: 3.663A pdb=" N VAL D2611 " --> pdb=" O MET D2608 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 153 removed outlier: 3.752A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 131 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU A 124 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N VAL A 135 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 13.299A pdb=" N ILE A 122 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 153 removed outlier: 3.752A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 131 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU A 124 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N VAL A 135 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 13.299A pdb=" N ILE A 122 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN A 222 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR A 17 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.673A pdb=" N VAL A 37 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AA5, first strand: chain 'A' and resid 304 through 308 removed outlier: 3.650A pdb=" N VAL A 241 " --> pdb=" O TRP A 283 " (cutoff:3.500A) removed outlier: 14.295A pdb=" N VAL A 241 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N CYS A 254 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU A 243 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE A 251 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 266 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 20.664A pdb=" N LEU A 261 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 15.151A pdb=" N THR A 419 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL A 263 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU A 417 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL A 403 " --> pdb=" O MET A 416 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY A 418 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N THR A 401 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N CYS A 420 " --> pdb=" O GLN A 399 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLN A 399 " --> pdb=" O CYS A 420 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 304 through 308 removed outlier: 3.650A pdb=" N VAL A 241 " --> pdb=" O TRP A 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 314 through 318 Processing sheet with id=AA8, first strand: chain 'A' and resid 367 through 370 Processing sheet with id=AA9, first strand: chain 'A' and resid 667 through 670 Processing sheet with id=AB1, first strand: chain 'A' and resid 2121 through 2124 Processing sheet with id=AB2, first strand: chain 'A' and resid 2396 through 2398 Processing sheet with id=AB3, first strand: chain 'B' and resid 668 through 669 removed outlier: 4.101A pdb=" N LEU B 694 " --> pdb=" O LYS B 706 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 706 " --> pdb=" O LEU B 694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2121 through 2124 Processing sheet with id=AB5, first strand: chain 'B' and resid 2396 through 2398 Processing sheet with id=AB6, first strand: chain 'C' and resid 667 through 670 removed outlier: 3.794A pdb=" N LEU C 694 " --> pdb=" O LYS C 706 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 706 " --> pdb=" O LEU C 694 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 800 through 801 Processing sheet with id=AB8, first strand: chain 'C' and resid 2121 through 2124 Processing sheet with id=AB9, first strand: chain 'C' and resid 2396 through 2398 Processing sheet with id=AC1, first strand: chain 'D' and resid 13 through 14 removed outlier: 14.668A pdb=" N ILE D 122 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N VAL D 135 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU D 124 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 133 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS D 126 " --> pdb=" O LYS D 131 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D 131 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N VAL D 135 " --> pdb=" O ASP D 153 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N ASP D 153 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N LYS D 137 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N THR D 151 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU D 139 " --> pdb=" O ARG D 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AC3, first strand: chain 'D' and resid 17 through 19 Processing sheet with id=AC4, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.609A pdb=" N LYS D 208 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 305 through 308 removed outlier: 15.206A pdb=" N VAL D 241 " --> pdb=" O CYS D 254 " (cutoff:3.500A) removed outlier: 11.185A pdb=" N CYS D 254 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU D 243 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 252 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N PHE D 251 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D 266 " --> pdb=" O PHE D 251 " (cutoff:3.500A) removed outlier: 21.954A pdb=" N LEU D 261 " --> pdb=" O THR D 419 " (cutoff:3.500A) removed outlier: 16.524A pdb=" N THR D 419 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N VAL D 263 " --> pdb=" O LEU D 417 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU D 417 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ARG D 414 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 403 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET D 416 " --> pdb=" O THR D 401 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU D 389 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N SER D 400 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 16.427A pdb=" N VAL D 387 " --> pdb=" O SER D 400 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 305 through 308 Processing sheet with id=AC7, first strand: chain 'D' and resid 314 through 318 Processing sheet with id=AC8, first strand: chain 'D' and resid 667 through 670 removed outlier: 4.061A pdb=" N ARG D 667 " --> pdb=" O THR D 695 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 800 through 801 removed outlier: 3.817A pdb=" N ARG D 801 " --> pdb=" O GLN D1096 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 2121 through 2124 Processing sheet with id=AD2, first strand: chain 'D' and resid 2396 through 2398 3632 hydrogen bonds defined for protein. 10551 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: 12.90 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 16062 1.34 - 1.46: 9276 1.46 - 1.58: 19274 1.58 - 1.70: 22 1.70 - 1.82: 184 Bond restraints: 44818 Sorted by residual: bond pdb=" O4 I3P D2702 " pdb=" P4 I3P D2702 " ideal model delta sigma weight residual 1.697 1.648 0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" O4 I3P A2702 " pdb=" P4 I3P A2702 " ideal model delta sigma weight residual 1.697 1.648 0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" O5 I3P A2702 " pdb=" P5 I3P A2702 " ideal model delta sigma weight residual 1.695 1.648 0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" O5 I3P D2702 " pdb=" P5 I3P D2702 " ideal model delta sigma weight residual 1.695 1.648 0.047 2.00e-02 2.50e+03 5.41e+00 bond pdb=" O1 I3P D2702 " pdb=" P1 I3P D2702 " ideal model delta sigma weight residual 1.691 1.647 0.044 2.00e-02 2.50e+03 4.84e+00 ... (remaining 44813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 60940 1.72 - 3.44: 476 3.44 - 5.17: 72 5.17 - 6.89: 29 6.89 - 8.61: 7 Bond angle restraints: 61524 Sorted by residual: angle pdb=" C ASP B 742 " pdb=" CA ASP B 742 " pdb=" CB ASP B 742 " ideal model delta sigma weight residual 117.23 111.38 5.85 1.36e+00 5.41e-01 1.85e+01 angle pdb=" N VAL A2577 " pdb=" CA VAL A2577 " pdb=" C VAL A2577 " ideal model delta sigma weight residual 113.20 109.74 3.46 9.60e-01 1.09e+00 1.30e+01 angle pdb=" CA GLN A2066 " pdb=" CB GLN A2066 " pdb=" CG GLN A2066 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.80e+00 angle pdb=" N ILE B2479 " pdb=" CA ILE B2479 " pdb=" C ILE B2479 " ideal model delta sigma weight residual 112.96 109.84 3.12 1.00e+00 1.00e+00 9.71e+00 angle pdb=" N ILE C1869 " pdb=" CA ILE C1869 " pdb=" C ILE C1869 " ideal model delta sigma weight residual 112.29 109.48 2.81 9.40e-01 1.13e+00 8.93e+00 ... (remaining 61519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.48: 25732 22.48 - 44.96: 895 44.96 - 67.45: 118 67.45 - 89.93: 27 89.93 - 112.41: 16 Dihedral angle restraints: 26788 sinusoidal: 5531 harmonic: 21257 Sorted by residual: dihedral pdb=" CB CYS A2455 " pdb=" SG CYS A2455 " pdb=" SG CYS A2461 " pdb=" CB CYS A2461 " ideal model delta sinusoidal sigma weight residual 93.00 161.52 -68.52 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS B2455 " pdb=" SG CYS B2455 " pdb=" SG CYS B2461 " pdb=" CB CYS B2461 " ideal model delta sinusoidal sigma weight residual 93.00 160.38 -67.38 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS D2455 " pdb=" SG CYS D2455 " pdb=" SG CYS D2461 " pdb=" CB CYS D2461 " ideal model delta sinusoidal sigma weight residual 93.00 159.71 -66.71 1 1.00e+01 1.00e-02 5.80e+01 ... (remaining 26785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 6907 0.059 - 0.117: 992 0.117 - 0.176: 38 0.176 - 0.234: 0 0.234 - 0.293: 12 Chirality restraints: 7949 Sorted by residual: chirality pdb=" C3' ATP B2702 " pdb=" C2' ATP B2702 " pdb=" C4' ATP B2702 " pdb=" O3' ATP B2702 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C3' ATP A2703 " pdb=" C2' ATP A2703 " pdb=" C4' ATP A2703 " pdb=" O3' ATP A2703 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C3' ATP D2703 " pdb=" C2' ATP D2703 " pdb=" C4' ATP D2703 " pdb=" O3' ATP D2703 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 7946 not shown) Planarity restraints: 8238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D2279 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO D2280 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO D2280 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D2280 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A2279 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A2280 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A2280 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2280 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A2066 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" CD GLN A2066 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLN A2066 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN A2066 " -0.011 2.00e-02 2.50e+03 ... (remaining 8235 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 286 2.55 - 3.14: 38865 3.14 - 3.73: 71354 3.73 - 4.31: 81953 4.31 - 4.90: 138299 Nonbonded interactions: 330757 Sorted by model distance: nonbonded pdb=" OD1 ASP B1968 " pdb=" OG SER B2019 " model vdw 1.968 3.040 nonbonded pdb=" O LEU C2155 " pdb=" OG1 THR C2159 " model vdw 1.988 3.040 nonbonded pdb=" O VAL C2575 " pdb=" OH TYR C2583 " model vdw 1.991 3.040 nonbonded pdb=" O LEU D2155 " pdb=" OG1 THR D2159 " model vdw 2.040 3.040 nonbonded pdb=" O VAL D2575 " pdb=" OH TYR D2583 " model vdw 2.061 3.040 ... (remaining 330752 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 'A' and (resid 5 through 289 or resid 304 through 1308 or resid 1319 thro \ ugh 1417 or resid 1436 through 1913 or resid 1926 or resid 1932 through 1975 or \ resid 1987 through 2704)) selection = (chain 'D' and (resid 5 through 1913 or resid 1916 or resid 1932 through 2006 or \ resid 2012 through 2704)) } ncs_group { reference = (chain 'B' and (resid 437 through 1305 or resid 1319 through 1420 or (resid 1589 \ through 1731 and (name N or name CA or name C or name O or name CB )) or (resid \ 1732 through 1740 and (name N or name CA or name C or name O or name CB )) or ( \ resid 1751 through 1754 and (name N or name CA or name C or name O or name CB )) \ or resid 1755 or (resid 1756 through 1762 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1763 through 1764 or (resid 1765 through 1800 and ( \ name N or name CA or name C or name O or name CB )) or resid 1865 through 2703)) \ selection = (chain 'C' and (resid 437 through 486 or resid 503 through 1099 or resid 1101 th \ rough 1776 or resid 1783 through 1893 or resid 1902 through 2703)) } 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 group one per residue 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: 9.420 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: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 51.410 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 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 : 0.002 0.049 44838 Z= 0.101 Angle : 0.456 8.610 61536 Z= 0.260 Chirality : 0.037 0.293 7949 Planarity : 0.003 0.053 8238 Dihedral : 12.943 112.409 12776 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.11), residues: 7069 helix: 2.54 (0.08), residues: 4695 sheet: -1.06 (0.31), residues: 313 loop : -1.44 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C2007 TYR 0.015 0.001 TYR A1947 PHE 0.012 0.001 PHE C2340 TRP 0.013 0.001 TRP B2566 HIS 0.006 0.001 HIS B2063 Details of bonding type rmsd covalent geometry : bond 0.00200 (44818) covalent geometry : angle 0.45364 (61524) SS BOND : bond 0.00226 ( 4) SS BOND : angle 3.74799 ( 8) hydrogen bonds : bond 0.14770 ( 3604) hydrogen bonds : angle 5.61604 (10551) metal coordination : bond 0.00287 ( 16) metal coordination : angle 2.74072 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 977 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1992 LEU cc_start: 0.7922 (mp) cc_final: 0.7549 (tt) REVERT: A 2200 ARG cc_start: 0.7556 (mtt90) cc_final: 0.7066 (mtt90) REVERT: A 2326 TYR cc_start: 0.7586 (t80) cc_final: 0.7194 (t80) REVERT: A 2540 ILE cc_start: 0.8398 (mm) cc_final: 0.7969 (mm) REVERT: B 1736 LEU cc_start: 0.7596 (tp) cc_final: 0.7203 (mp) REVERT: B 1925 LEU cc_start: 0.6569 (mt) cc_final: 0.5976 (pp) REVERT: B 1952 CYS cc_start: 0.8214 (t) cc_final: 0.7638 (t) REVERT: B 2012 ASN cc_start: 0.8326 (m110) cc_final: 0.7968 (m110) REVERT: B 2195 TYR cc_start: 0.8086 (t80) cc_final: 0.7552 (t80) REVERT: B 2204 TRP cc_start: 0.7692 (m100) cc_final: 0.7345 (m100) REVERT: B 2269 ILE cc_start: 0.8823 (mm) cc_final: 0.8508 (mm) REVERT: B 2326 TYR cc_start: 0.7955 (t80) cc_final: 0.7567 (t80) REVERT: B 2554 SER cc_start: 0.8371 (t) cc_final: 0.8003 (p) REVERT: C 2128 ARG cc_start: 0.6681 (mmm-85) cc_final: 0.6273 (mmm-85) REVERT: C 2182 MET cc_start: 0.7269 (mtp) cc_final: 0.6891 (mtp) REVERT: C 2557 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6229 (tm-30) REVERT: D 1744 THR cc_start: 0.8039 (t) cc_final: 0.7618 (p) REVERT: D 1783 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7386 (tt0) REVERT: D 1791 ASP cc_start: 0.7515 (m-30) cc_final: 0.7263 (t70) REVERT: D 1882 GLU cc_start: 0.7667 (tp30) cc_final: 0.7335 (tp30) REVERT: D 1890 ASN cc_start: 0.7330 (m-40) cc_final: 0.6976 (p0) REVERT: D 1901 TYR cc_start: 0.5807 (m-10) cc_final: 0.5215 (m-80) REVERT: D 1999 LEU cc_start: 0.8039 (tp) cc_final: 0.7819 (tp) REVERT: D 2017 LEU cc_start: 0.8651 (mt) cc_final: 0.8438 (mt) REVERT: D 2063 HIS cc_start: 0.7670 (m-70) cc_final: 0.7468 (m170) REVERT: D 2164 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7198 (tp40) outliers start: 0 outliers final: 0 residues processed: 977 average time/residue: 0.2470 time to fit residues: 406.4763 Evaluate side-chains 717 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 717 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 394 optimal weight: 50.0000 chunk 430 optimal weight: 50.0000 chunk 41 optimal weight: 30.0000 chunk 265 optimal weight: 50.0000 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 50.0000 chunk 310 optimal weight: 0.7980 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 0.9980 chunk 597 optimal weight: 20.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1797 GLN A1896 ASN A2135 GLN A2164 GLN A2210 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2468 HIS A2472 ASN ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2323 HIS B2468 HIS ** C1871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1939 GLN C1962 HIS ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2468 HIS D1798 GLN D1885 ASN ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.209662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.180624 restraints weight = 81757.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.176451 restraints weight = 108739.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.171582 restraints weight = 94025.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.168423 restraints weight = 100519.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.167239 restraints weight = 81128.961| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 44838 Z= 0.340 Angle : 0.723 14.270 61536 Z= 0.378 Chirality : 0.044 0.245 7949 Planarity : 0.004 0.064 8238 Dihedral : 6.237 85.913 7595 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.66 % Allowed : 14.90 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.11), residues: 7069 helix: 2.14 (0.08), residues: 4856 sheet: -1.16 (0.31), residues: 305 loop : -1.41 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C2189 TYR 0.029 0.002 TYR D1901 PHE 0.032 0.003 PHE A1876 TRP 0.021 0.002 TRP C2601 HIS 0.011 0.002 HIS A1884 Details of bonding type rmsd covalent geometry : bond 0.00810 (44818) covalent geometry : angle 0.71952 (61524) SS BOND : bond 0.01587 ( 4) SS BOND : angle 3.19033 ( 8) hydrogen bonds : bond 0.04419 ( 3604) hydrogen bonds : angle 4.43820 (10551) metal coordination : bond 0.01987 ( 16) metal coordination : angle 7.48826 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 727 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1783 GLU cc_start: 0.7307 (tp30) cc_final: 0.6247 (tp30) REVERT: A 2593 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7528 (mtt) REVERT: B 1730 LYS cc_start: 0.7423 (pttp) cc_final: 0.7000 (pttp) REVERT: B 1765 ASN cc_start: 0.7591 (t0) cc_final: 0.7316 (m-40) REVERT: B 1888 LEU cc_start: 0.8703 (mt) cc_final: 0.8486 (mm) REVERT: B 2191 MET cc_start: 0.8039 (mmm) cc_final: 0.7205 (mtm) REVERT: B 2269 ILE cc_start: 0.8745 (mm) cc_final: 0.8519 (mm) REVERT: B 2554 SER cc_start: 0.8970 (t) cc_final: 0.8640 (p) REVERT: B 2592 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8204 (tm-30) REVERT: C 1958 CYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6526 (p) REVERT: C 2054 TYR cc_start: 0.7101 (t80) cc_final: 0.6867 (t80) REVERT: C 2175 SER cc_start: 0.8737 (p) cc_final: 0.8500 (t) REVERT: C 2261 ILE cc_start: 0.6765 (pt) cc_final: 0.6511 (mt) REVERT: C 2549 ASP cc_start: 0.7282 (p0) cc_final: 0.6957 (p0) REVERT: D 1726 CYS cc_start: 0.8519 (p) cc_final: 0.8231 (p) REVERT: D 1727 ARG cc_start: 0.7840 (tpt-90) cc_final: 0.7402 (tpp80) REVERT: D 1785 PHE cc_start: 0.7791 (t80) cc_final: 0.7567 (t80) REVERT: D 1876 PHE cc_start: 0.8579 (t80) cc_final: 0.8373 (t80) REVERT: D 1882 GLU cc_start: 0.8224 (tp30) cc_final: 0.7976 (tp30) REVERT: D 1896 ASN cc_start: 0.7434 (m-40) cc_final: 0.6586 (p0) REVERT: D 1960 VAL cc_start: 0.7614 (m) cc_final: 0.7234 (t) REVERT: D 2026 VAL cc_start: 0.8121 (p) cc_final: 0.7792 (t) REVERT: D 2063 HIS cc_start: 0.7750 (m-70) cc_final: 0.7400 (m-70) REVERT: D 2130 ASP cc_start: 0.7585 (p0) cc_final: 0.7372 (p0) outliers start: 111 outliers final: 75 residues processed: 797 average time/residue: 0.2351 time to fit residues: 323.2841 Evaluate side-chains 717 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 640 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1905 CYS Chi-restraints excluded: chain A residue 2018 ILE Chi-restraints excluded: chain A residue 2061 SER Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2127 VAL Chi-restraints excluded: chain A residue 2159 THR Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2329 THR Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain A residue 2593 MET Chi-restraints excluded: chain B residue 1728 LEU Chi-restraints excluded: chain B residue 1904 VAL Chi-restraints excluded: chain B residue 1924 LEU Chi-restraints excluded: chain B residue 2026 VAL Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2295 VAL Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2451 THR Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2581 THR Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1952 CYS Chi-restraints excluded: chain C residue 1955 ASN Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2006 SER Chi-restraints excluded: chain C residue 2127 VAL Chi-restraints excluded: chain C residue 2135 GLN Chi-restraints excluded: chain C residue 2152 LYS Chi-restraints excluded: chain C residue 2203 LEU Chi-restraints excluded: chain C residue 2290 LEU Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2503 ILE Chi-restraints excluded: chain C residue 2506 ILE Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 1734 THR Chi-restraints excluded: chain D residue 1798 GLN Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1911 LEU Chi-restraints excluded: chain D residue 1952 CYS Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 1975 LEU Chi-restraints excluded: chain D residue 1988 LEU Chi-restraints excluded: chain D residue 1989 VAL Chi-restraints excluded: chain D residue 1993 LYS Chi-restraints excluded: chain D residue 2067 LEU Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2283 ASN Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2362 VAL Chi-restraints excluded: chain D residue 2371 LEU Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2523 LEU Chi-restraints excluded: chain D residue 2526 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 275 optimal weight: 50.0000 chunk 182 optimal weight: 0.9980 chunk 545 optimal weight: 30.0000 chunk 360 optimal weight: 0.9980 chunk 1 optimal weight: 50.0000 chunk 415 optimal weight: 8.9990 chunk 696 optimal weight: 0.5980 chunk 680 optimal weight: 0.4980 chunk 533 optimal weight: 50.0000 chunk 593 optimal weight: 50.0000 chunk 707 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1774 ASN A2210 ASN A2216 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2550 ASN B1773 HIS ** B1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2210 ASN C1871 GLN C2119 ASN C2123 GLN C2135 GLN ** C2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1773 HIS ** D1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1884 HIS D1900 ASN ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.213765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.184027 restraints weight = 83424.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.180219 restraints weight = 96356.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.176727 restraints weight = 83619.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.176447 restraints weight = 76694.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.174725 restraints weight = 58850.794| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 44838 Z= 0.113 Angle : 0.495 10.344 61536 Z= 0.263 Chirality : 0.038 0.211 7949 Planarity : 0.003 0.054 8238 Dihedral : 4.891 79.898 7595 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.77 % Allowed : 20.24 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.11), residues: 7069 helix: 2.52 (0.08), residues: 4859 sheet: -1.01 (0.31), residues: 305 loop : -1.11 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2186 TYR 0.017 0.001 TYR B1947 PHE 0.019 0.001 PHE C1910 TRP 0.012 0.001 TRP B2184 HIS 0.004 0.001 HIS A2063 Details of bonding type rmsd covalent geometry : bond 0.00249 (44818) covalent geometry : angle 0.49315 (61524) SS BOND : bond 0.00215 ( 4) SS BOND : angle 1.88621 ( 8) hydrogen bonds : bond 0.02963 ( 3604) hydrogen bonds : angle 3.79580 (10551) metal coordination : bond 0.00413 ( 16) metal coordination : angle 4.07678 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 725 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1783 GLU cc_start: 0.7314 (tp30) cc_final: 0.6869 (tp30) REVERT: A 1868 LEU cc_start: 0.7780 (mm) cc_final: 0.7524 (mt) REVERT: B 1793 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7651 (mtp) REVERT: B 2191 MET cc_start: 0.7866 (mmm) cc_final: 0.7025 (mtm) REVERT: B 2554 SER cc_start: 0.8802 (t) cc_final: 0.8419 (p) REVERT: C 2121 THR cc_start: 0.7297 (m) cc_final: 0.6761 (m) REVERT: C 2133 MET cc_start: 0.8200 (mmm) cc_final: 0.7934 (mmm) REVERT: C 2175 SER cc_start: 0.8699 (p) cc_final: 0.8466 (t) REVERT: C 2549 ASP cc_start: 0.7082 (p0) cc_final: 0.6740 (p0) REVERT: D 1726 CYS cc_start: 0.8293 (p) cc_final: 0.8051 (p) REVERT: D 1785 PHE cc_start: 0.7677 (t80) cc_final: 0.7428 (t80) REVERT: D 1882 GLU cc_start: 0.8173 (tp30) cc_final: 0.7776 (tt0) REVERT: D 1887 ASP cc_start: 0.7487 (m-30) cc_final: 0.7225 (m-30) REVERT: D 1896 ASN cc_start: 0.7284 (m-40) cc_final: 0.6471 (p0) REVERT: D 1902 ASN cc_start: 0.7288 (t0) cc_final: 0.6962 (t0) REVERT: D 1960 VAL cc_start: 0.7573 (m) cc_final: 0.7200 (t) REVERT: D 2026 VAL cc_start: 0.8170 (p) cc_final: 0.7696 (t) REVERT: D 2031 LYS cc_start: 0.7728 (mmmt) cc_final: 0.7315 (ttpp) REVERT: D 2130 ASP cc_start: 0.7729 (p0) cc_final: 0.7490 (p0) REVERT: D 2343 ILE cc_start: 0.9044 (mm) cc_final: 0.8836 (mm) REVERT: D 2561 LEU cc_start: 0.8047 (mt) cc_final: 0.7762 (mt) outliers start: 66 outliers final: 34 residues processed: 758 average time/residue: 0.2247 time to fit residues: 294.8790 Evaluate side-chains 682 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 647 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1954 GLU Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2523 LEU Chi-restraints excluded: chain A residue 2550 ASN Chi-restraints excluded: chain B residue 1728 LEU Chi-restraints excluded: chain B residue 1740 LEU Chi-restraints excluded: chain B residue 1788 VAL Chi-restraints excluded: chain B residue 1793 MET Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2301 VAL Chi-restraints excluded: chain B residue 2451 THR Chi-restraints excluded: chain C residue 1952 CYS Chi-restraints excluded: chain C residue 2006 SER Chi-restraints excluded: chain C residue 2069 HIS Chi-restraints excluded: chain C residue 2119 ASN Chi-restraints excluded: chain C residue 2203 LEU Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain D residue 1911 LEU Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 1989 VAL Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2362 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2534 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 276 optimal weight: 50.0000 chunk 607 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 269 optimal weight: 8.9990 chunk 707 optimal weight: 0.9990 chunk 370 optimal weight: 50.0000 chunk 98 optimal weight: 30.0000 chunk 175 optimal weight: 1.9990 chunk 93 optimal weight: 50.0000 chunk 492 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2210 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1883 ASN ** B1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1871 GLN C1883 ASN ** C1995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2135 GLN C2210 ASN ** C2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1798 GLN D1900 ASN ** D1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.211028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.173302 restraints weight = 82289.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.166438 restraints weight = 89340.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.163852 restraints weight = 64527.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.162319 restraints weight = 51450.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.161268 restraints weight = 45731.403| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 44838 Z= 0.149 Angle : 0.516 12.374 61536 Z= 0.271 Chirality : 0.039 0.200 7949 Planarity : 0.003 0.053 8238 Dihedral : 4.639 75.778 7595 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.79 % Allowed : 21.03 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.11), residues: 7069 helix: 2.58 (0.08), residues: 4845 sheet: -0.98 (0.31), residues: 305 loop : -1.00 (0.15), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2186 TYR 0.020 0.001 TYR B1947 PHE 0.019 0.001 PHE D1876 TRP 0.010 0.001 TRP B2184 HIS 0.005 0.001 HIS A1884 Details of bonding type rmsd covalent geometry : bond 0.00347 (44818) covalent geometry : angle 0.51403 (61524) SS BOND : bond 0.00523 ( 4) SS BOND : angle 1.75114 ( 8) hydrogen bonds : bond 0.02948 ( 3604) hydrogen bonds : angle 3.65643 (10551) metal coordination : bond 0.00779 ( 16) metal coordination : angle 4.26368 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 676 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1783 GLU cc_start: 0.7417 (tp30) cc_final: 0.7035 (tp30) REVERT: A 1793 MET cc_start: 0.7955 (mtp) cc_final: 0.7735 (mtp) REVERT: A 1868 LEU cc_start: 0.7900 (mm) cc_final: 0.7583 (mt) REVERT: A 2014 GLU cc_start: 0.5956 (pm20) cc_final: 0.5725 (pm20) REVERT: A 2183 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6783 (tm-30) REVERT: A 2201 MET cc_start: 0.8726 (tpp) cc_final: 0.8366 (tpp) REVERT: B 1725 GLN cc_start: 0.8128 (mt0) cc_final: 0.7749 (mt0) REVERT: B 1740 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8112 (mt) REVERT: B 1793 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7719 (mtp) REVERT: B 2191 MET cc_start: 0.7886 (mmm) cc_final: 0.7045 (mtm) REVERT: B 2554 SER cc_start: 0.8851 (t) cc_final: 0.8393 (p) REVERT: C 1993 LYS cc_start: 0.6110 (mttm) cc_final: 0.5718 (mmmm) REVERT: C 2135 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6774 (tm-30) REVERT: C 2549 ASP cc_start: 0.7028 (p0) cc_final: 0.6770 (p0) REVERT: D 1726 CYS cc_start: 0.8478 (p) cc_final: 0.8221 (p) REVERT: D 1727 ARG cc_start: 0.7900 (mmt180) cc_final: 0.7592 (tpp80) REVERT: D 1785 PHE cc_start: 0.8060 (t80) cc_final: 0.7756 (t80) REVERT: D 1887 ASP cc_start: 0.7619 (m-30) cc_final: 0.7359 (m-30) REVERT: D 1896 ASN cc_start: 0.7205 (m-40) cc_final: 0.6496 (p0) REVERT: D 1960 VAL cc_start: 0.7894 (m) cc_final: 0.7597 (p) REVERT: D 2026 VAL cc_start: 0.8329 (p) cc_final: 0.8066 (t) REVERT: D 2031 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7391 (ttpp) REVERT: D 2063 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.6972 (t-90) REVERT: D 2130 ASP cc_start: 0.7843 (p0) cc_final: 0.7608 (p0) REVERT: D 2561 LEU cc_start: 0.8011 (mt) cc_final: 0.7651 (mt) outliers start: 114 outliers final: 78 residues processed: 742 average time/residue: 0.2297 time to fit residues: 295.1867 Evaluate side-chains 711 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 629 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1952 CYS Chi-restraints excluded: chain A residue 1954 GLU Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 2004 MET Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2264 LEU Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2479 ILE Chi-restraints excluded: chain A residue 2523 LEU Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain B residue 1740 LEU Chi-restraints excluded: chain B residue 1745 LYS Chi-restraints excluded: chain B residue 1788 VAL Chi-restraints excluded: chain B residue 1793 MET Chi-restraints excluded: chain B residue 1892 LEU Chi-restraints excluded: chain B residue 1924 LEU Chi-restraints excluded: chain B residue 1989 VAL Chi-restraints excluded: chain B residue 2008 HIS Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2218 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2301 VAL Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2451 THR Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2581 THR Chi-restraints excluded: chain B residue 2608 MET Chi-restraints excluded: chain C residue 1883 ASN Chi-restraints excluded: chain C residue 1952 CYS Chi-restraints excluded: chain C residue 1955 ASN Chi-restraints excluded: chain C residue 2069 HIS Chi-restraints excluded: chain C residue 2127 VAL Chi-restraints excluded: chain C residue 2135 GLN Chi-restraints excluded: chain C residue 2203 LEU Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2505 ILE Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2594 ILE Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 1721 ILE Chi-restraints excluded: chain D residue 1724 THR Chi-restraints excluded: chain D residue 1782 SER Chi-restraints excluded: chain D residue 1880 LEU Chi-restraints excluded: chain D residue 1903 LEU Chi-restraints excluded: chain D residue 1908 LEU Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1940 THR Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 1989 VAL Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2063 HIS Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2328 LEU Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2362 VAL Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2503 ILE Chi-restraints excluded: chain D residue 2526 GLU Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2549 ASP Chi-restraints excluded: chain D residue 2554 SER Chi-restraints excluded: chain D residue 2573 VAL Chi-restraints excluded: chain D residue 2575 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 211 optimal weight: 50.0000 chunk 654 optimal weight: 50.0000 chunk 111 optimal weight: 50.0000 chunk 505 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 427 optimal weight: 50.0000 chunk 398 optimal weight: 0.9990 chunk 679 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 28 optimal weight: 50.0000 chunk 521 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1976 ASN A2135 GLN A2210 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2023 GLN B2292 ASN C1871 GLN C1953 HIS ** C1995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2012 ASN ** C2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1797 GLN D1798 GLN D1900 ASN D1953 HIS ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.209748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.175042 restraints weight = 82211.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.171137 restraints weight = 99953.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.160107 restraints weight = 74056.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.153805 restraints weight = 55481.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152212 restraints weight = 55057.112| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 44838 Z= 0.185 Angle : 0.547 13.572 61536 Z= 0.286 Chirality : 0.039 0.227 7949 Planarity : 0.003 0.058 8238 Dihedral : 4.612 74.219 7595 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.67 % Allowed : 21.79 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.11), residues: 7069 helix: 2.56 (0.08), residues: 4860 sheet: -1.06 (0.30), residues: 333 loop : -1.02 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D2021 TYR 0.030 0.002 TYR C2054 PHE 0.029 0.002 PHE B1910 TRP 0.011 0.001 TRP C2601 HIS 0.009 0.001 HIS C1884 Details of bonding type rmsd covalent geometry : bond 0.00440 (44818) covalent geometry : angle 0.54570 (61524) SS BOND : bond 0.00804 ( 4) SS BOND : angle 1.61171 ( 8) hydrogen bonds : bond 0.03066 ( 3604) hydrogen bonds : angle 3.63232 (10551) metal coordination : bond 0.00986 ( 16) metal coordination : angle 4.99219 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 645 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1783 GLU cc_start: 0.7399 (tp30) cc_final: 0.7059 (tp30) REVERT: A 2183 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6869 (tm-30) REVERT: B 1906 GLU cc_start: 0.6406 (mm-30) cc_final: 0.6183 (mm-30) REVERT: B 2191 MET cc_start: 0.7831 (mmm) cc_final: 0.7116 (mtm) REVERT: B 2554 SER cc_start: 0.8808 (t) cc_final: 0.8403 (p) REVERT: C 1893 ARG cc_start: 0.3648 (ttp-110) cc_final: 0.3151 (tpt90) REVERT: C 1925 LEU cc_start: 0.6186 (pp) cc_final: 0.5777 (mm) REVERT: C 1931 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6585 (mp0) REVERT: C 1958 CYS cc_start: 0.7185 (m) cc_final: 0.6863 (p) REVERT: C 1993 LYS cc_start: 0.6365 (mttm) cc_final: 0.5948 (mmmm) REVERT: C 2135 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7227 (mm-40) REVERT: D 1726 CYS cc_start: 0.8824 (p) cc_final: 0.8557 (p) REVERT: D 1727 ARG cc_start: 0.8531 (mmt180) cc_final: 0.8205 (tpp80) REVERT: D 1745 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7420 (mmtt) REVERT: D 1784 ARG cc_start: 0.8921 (tpp80) cc_final: 0.8606 (tpt90) REVERT: D 1785 PHE cc_start: 0.8590 (t80) cc_final: 0.8120 (t80) REVERT: D 1887 ASP cc_start: 0.7795 (m-30) cc_final: 0.7502 (m-30) REVERT: D 1896 ASN cc_start: 0.7217 (m-40) cc_final: 0.6671 (p0) REVERT: D 1960 VAL cc_start: 0.8293 (m) cc_final: 0.8005 (p) REVERT: D 2026 VAL cc_start: 0.8337 (p) cc_final: 0.7979 (t) REVERT: D 2031 LYS cc_start: 0.8025 (mmmt) cc_final: 0.7536 (ttpp) REVERT: D 2063 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7073 (t-90) REVERT: D 2130 ASP cc_start: 0.7879 (p0) cc_final: 0.7679 (p0) REVERT: D 2561 LEU cc_start: 0.8071 (mt) cc_final: 0.7604 (mt) outliers start: 135 outliers final: 96 residues processed: 735 average time/residue: 0.2384 time to fit residues: 302.2524 Evaluate side-chains 705 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 607 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1800 THR Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1952 CYS Chi-restraints excluded: chain A residue 1965 ASN Chi-restraints excluded: chain A residue 1973 LEU Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2194 ILE Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2264 LEU Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2455 CYS Chi-restraints excluded: chain A residue 2523 LEU Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain A residue 2593 MET Chi-restraints excluded: chain B residue 1728 LEU Chi-restraints excluded: chain B residue 1788 VAL Chi-restraints excluded: chain B residue 1989 VAL Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2070 LEU Chi-restraints excluded: chain B residue 2072 LYS Chi-restraints excluded: chain B residue 2218 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2451 THR Chi-restraints excluded: chain B residue 2455 CYS Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2479 ILE Chi-restraints excluded: chain B residue 2504 VAL Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2581 THR Chi-restraints excluded: chain B residue 2608 MET Chi-restraints excluded: chain C residue 1883 ASN Chi-restraints excluded: chain C residue 1952 CYS Chi-restraints excluded: chain C residue 1955 ASN Chi-restraints excluded: chain C residue 2068 GLN Chi-restraints excluded: chain C residue 2069 HIS Chi-restraints excluded: chain C residue 2135 GLN Chi-restraints excluded: chain C residue 2203 LEU Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2290 LEU Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2503 ILE Chi-restraints excluded: chain C residue 2505 ILE Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain C residue 2594 ILE Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 1721 ILE Chi-restraints excluded: chain D residue 1724 THR Chi-restraints excluded: chain D residue 1738 CYS Chi-restraints excluded: chain D residue 1880 LEU Chi-restraints excluded: chain D residue 1903 LEU Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1908 LEU Chi-restraints excluded: chain D residue 1911 LEU Chi-restraints excluded: chain D residue 1934 VAL Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1956 GLN Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 1989 VAL Chi-restraints excluded: chain D residue 2063 HIS Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2278 ILE Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2362 VAL Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2455 CYS Chi-restraints excluded: chain D residue 2503 ILE Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2523 LEU Chi-restraints excluded: chain D residue 2526 GLU Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2549 ASP Chi-restraints excluded: chain D residue 2573 VAL Chi-restraints excluded: chain D residue 2575 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 290 optimal weight: 0.9990 chunk 417 optimal weight: 40.0000 chunk 532 optimal weight: 50.0000 chunk 552 optimal weight: 30.0000 chunk 372 optimal weight: 40.0000 chunk 691 optimal weight: 2.9990 chunk 203 optimal weight: 50.0000 chunk 713 optimal weight: 0.0470 chunk 177 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 324 optimal weight: 8.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2210 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2063 HIS B2468 HIS ** C1995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1953 HIS D2323 HIS ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.203577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.171982 restraints weight = 81954.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.168531 restraints weight = 113548.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.167151 restraints weight = 83230.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.165684 restraints weight = 88068.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.164061 restraints weight = 73725.160| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 44838 Z= 0.260 Angle : 0.637 12.986 61536 Z= 0.328 Chirality : 0.041 0.241 7949 Planarity : 0.003 0.059 8238 Dihedral : 4.807 73.750 7595 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.30 % Allowed : 22.12 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.11), residues: 7069 helix: 2.41 (0.08), residues: 4883 sheet: -1.14 (0.31), residues: 296 loop : -1.16 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D2021 TYR 0.029 0.002 TYR C2054 PHE 0.037 0.002 PHE D1876 TRP 0.015 0.002 TRP C2601 HIS 0.011 0.002 HIS D1790 Details of bonding type rmsd covalent geometry : bond 0.00620 (44818) covalent geometry : angle 0.63403 (61524) SS BOND : bond 0.01215 ( 4) SS BOND : angle 1.77973 ( 8) hydrogen bonds : bond 0.03495 ( 3604) hydrogen bonds : angle 3.79802 (10551) metal coordination : bond 0.01669 ( 16) metal coordination : angle 6.70913 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 637 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1783 GLU cc_start: 0.7401 (tp30) cc_final: 0.6583 (tp30) REVERT: A 1793 MET cc_start: 0.8195 (mtp) cc_final: 0.7921 (mtp) REVERT: A 2181 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: A 2183 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6958 (tm-30) REVERT: B 2023 GLN cc_start: 0.8725 (tp40) cc_final: 0.8399 (tp-100) REVERT: B 2191 MET cc_start: 0.7771 (mmm) cc_final: 0.7030 (mtm) REVERT: B 2554 SER cc_start: 0.9052 (t) cc_final: 0.8645 (p) REVERT: C 1893 ARG cc_start: 0.3460 (ttp-110) cc_final: 0.2742 (tpt90) REVERT: C 1998 LYS cc_start: 0.7143 (ptpp) cc_final: 0.6665 (mmtm) REVERT: C 2054 TYR cc_start: 0.7040 (t80) cc_final: 0.6587 (t80) REVERT: C 2133 MET cc_start: 0.8448 (mmm) cc_final: 0.8211 (mmm) REVERT: C 2155 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9111 (mm) REVERT: C 2549 ASP cc_start: 0.6784 (p0) cc_final: 0.6515 (p0) REVERT: D 1727 ARG cc_start: 0.7816 (mmt180) cc_final: 0.7526 (tpp80) REVERT: D 1785 PHE cc_start: 0.7596 (t80) cc_final: 0.7384 (t80) REVERT: D 1795 ARG cc_start: 0.6788 (ttt180) cc_final: 0.6405 (ttp-170) REVERT: D 1870 MET cc_start: 0.6825 (tpp) cc_final: 0.6249 (tpp) REVERT: D 1887 ASP cc_start: 0.7568 (m-30) cc_final: 0.7362 (m-30) REVERT: D 1896 ASN cc_start: 0.6896 (m-40) cc_final: 0.6493 (p0) REVERT: D 1960 VAL cc_start: 0.8000 (m) cc_final: 0.7735 (p) REVERT: D 2026 VAL cc_start: 0.8349 (p) cc_final: 0.8112 (t) REVERT: D 2031 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7536 (ttpp) REVERT: D 2063 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6891 (t-90) REVERT: D 2130 ASP cc_start: 0.8055 (p0) cc_final: 0.7854 (p0) outliers start: 150 outliers final: 119 residues processed: 744 average time/residue: 0.2321 time to fit residues: 299.4403 Evaluate side-chains 722 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 600 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1800 THR Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1888 LEU Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1952 CYS Chi-restraints excluded: chain A residue 1965 ASN Chi-restraints excluded: chain A residue 1973 LEU Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2194 ILE Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2264 LEU Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2288 LEU Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2455 CYS Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2506 ILE Chi-restraints excluded: chain A residue 2523 LEU Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain A residue 2593 MET Chi-restraints excluded: chain B residue 1728 LEU Chi-restraints excluded: chain B residue 1729 ASP Chi-restraints excluded: chain B residue 1745 LYS Chi-restraints excluded: chain B residue 1754 ILE Chi-restraints excluded: chain B residue 1869 ILE Chi-restraints excluded: chain B residue 1904 VAL Chi-restraints excluded: chain B residue 1959 ILE Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2070 LEU Chi-restraints excluded: chain B residue 2218 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2371 LEU Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2451 THR Chi-restraints excluded: chain B residue 2455 CYS Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2504 VAL Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2556 GLU Chi-restraints excluded: chain B residue 2577 VAL Chi-restraints excluded: chain B residue 2608 MET Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1952 CYS Chi-restraints excluded: chain C residue 1955 ASN Chi-restraints excluded: chain C residue 2056 LEU Chi-restraints excluded: chain C residue 2068 GLN Chi-restraints excluded: chain C residue 2069 HIS Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2203 LEU Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2290 LEU Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2503 ILE Chi-restraints excluded: chain C residue 2505 ILE Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 1721 ILE Chi-restraints excluded: chain D residue 1880 LEU Chi-restraints excluded: chain D residue 1903 LEU Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1956 GLN Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 1989 VAL Chi-restraints excluded: chain D residue 2063 HIS Chi-restraints excluded: chain D residue 2067 LEU Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2121 THR Chi-restraints excluded: chain D residue 2127 VAL Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2278 ILE Chi-restraints excluded: chain D residue 2284 ILE Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2353 GLU Chi-restraints excluded: chain D residue 2362 VAL Chi-restraints excluded: chain D residue 2371 LEU Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2455 CYS Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2488 SER Chi-restraints excluded: chain D residue 2503 ILE Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2523 LEU Chi-restraints excluded: chain D residue 2526 GLU Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2549 ASP Chi-restraints excluded: chain D residue 2554 SER Chi-restraints excluded: chain D residue 2573 VAL Chi-restraints excluded: chain D residue 2575 VAL Chi-restraints excluded: chain D residue 2609 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 91 optimal weight: 50.0000 chunk 434 optimal weight: 0.0770 chunk 178 optimal weight: 0.8980 chunk 204 optimal weight: 50.0000 chunk 472 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 588 optimal weight: 50.0000 chunk 359 optimal weight: 0.9990 chunk 362 optimal weight: 5.9990 chunk 393 optimal weight: 50.0000 chunk 145 optimal weight: 0.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2210 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2472 ASN ** B1883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2216 ASN C1871 GLN C1995 ASN ** C2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2063 HIS ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1953 HIS ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.209947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.174185 restraints weight = 83171.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.169786 restraints weight = 91611.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.158482 restraints weight = 75689.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.156158 restraints weight = 58903.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.153427 restraints weight = 60133.328| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 44838 Z= 0.109 Angle : 0.501 14.923 61536 Z= 0.259 Chirality : 0.038 0.275 7949 Planarity : 0.003 0.061 8238 Dihedral : 4.461 71.137 7595 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.44 % Allowed : 25.69 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.11), residues: 7069 helix: 2.67 (0.07), residues: 4874 sheet: -1.00 (0.30), residues: 329 loop : -1.03 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D2021 TYR 0.032 0.001 TYR B1947 PHE 0.021 0.001 PHE D1876 TRP 0.015 0.001 TRP B2184 HIS 0.004 0.001 HIS D2558 Details of bonding type rmsd covalent geometry : bond 0.00244 (44818) covalent geometry : angle 0.49938 (61524) SS BOND : bond 0.00167 ( 4) SS BOND : angle 1.51545 ( 8) hydrogen bonds : bond 0.02606 ( 3604) hydrogen bonds : angle 3.44591 (10551) metal coordination : bond 0.00555 ( 16) metal coordination : angle 4.50543 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 654 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1783 GLU cc_start: 0.7208 (tp30) cc_final: 0.6306 (tp30) REVERT: A 2183 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6674 (tm-30) REVERT: B 2191 MET cc_start: 0.7634 (mmm) cc_final: 0.6892 (mtm) REVERT: B 2554 SER cc_start: 0.8897 (t) cc_final: 0.8370 (p) REVERT: C 1931 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6650 (mp0) REVERT: C 1953 HIS cc_start: 0.6107 (t70) cc_final: 0.5813 (t70) REVERT: C 1998 LYS cc_start: 0.7273 (ptpp) cc_final: 0.6962 (tppt) REVERT: C 2054 TYR cc_start: 0.6877 (t80) cc_final: 0.6315 (t80) REVERT: C 2063 HIS cc_start: 0.3491 (OUTLIER) cc_final: 0.2963 (m90) REVERT: C 2155 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9094 (mm) REVERT: C 2549 ASP cc_start: 0.6422 (p0) cc_final: 0.6168 (p0) REVERT: C 2593 MET cc_start: 0.8453 (mmt) cc_final: 0.8245 (mmt) REVERT: D 1727 ARG cc_start: 0.8700 (mmt180) cc_final: 0.8362 (tpp80) REVERT: D 1785 PHE cc_start: 0.8653 (t80) cc_final: 0.8198 (t80) REVERT: D 1960 VAL cc_start: 0.8384 (m) cc_final: 0.8124 (p) REVERT: D 2031 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7725 (ttpp) REVERT: D 2063 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.7129 (t-90) REVERT: D 2130 ASP cc_start: 0.7929 (p0) cc_final: 0.7725 (p0) outliers start: 82 outliers final: 60 residues processed: 707 average time/residue: 0.2228 time to fit residues: 270.9792 Evaluate side-chains 682 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 619 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2288 LEU Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2354 THR Chi-restraints excluded: chain A residue 2361 SER Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2455 CYS Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain B residue 1728 LEU Chi-restraints excluded: chain B residue 1745 LYS Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2070 LEU Chi-restraints excluded: chain B residue 2072 LYS Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2455 CYS Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2479 ILE Chi-restraints excluded: chain B residue 2504 VAL Chi-restraints excluded: chain B residue 2608 MET Chi-restraints excluded: chain C residue 1952 CYS Chi-restraints excluded: chain C residue 2063 HIS Chi-restraints excluded: chain C residue 2069 HIS Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2203 LEU Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2455 CYS Chi-restraints excluded: chain C residue 2505 ILE Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2525 SER Chi-restraints excluded: chain C residue 2590 VAL Chi-restraints excluded: chain D residue 1738 CYS Chi-restraints excluded: chain D residue 1880 LEU Chi-restraints excluded: chain D residue 1899 THR Chi-restraints excluded: chain D residue 1903 LEU Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1956 GLN Chi-restraints excluded: chain D residue 2063 HIS Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2362 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2455 CYS Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2549 ASP Chi-restraints excluded: chain D residue 2554 SER Chi-restraints excluded: chain D residue 2575 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 220 optimal weight: 1.9990 chunk 526 optimal weight: 50.0000 chunk 276 optimal weight: 50.0000 chunk 405 optimal weight: 40.0000 chunk 223 optimal weight: 20.0000 chunk 427 optimal weight: 50.0000 chunk 723 optimal weight: 0.8980 chunk 116 optimal weight: 40.0000 chunk 473 optimal weight: 20.0000 chunk 630 optimal weight: 50.0000 chunk 80 optimal weight: 30.0000 overall best weight: 14.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1774 ASN A1897 ASN ** A2064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2135 GLN A2210 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2063 HIS C1871 GLN C1897 ASN ** C1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2051 HIS ** C2063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1773 HIS ** D1897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1900 ASN D1953 HIS ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.190565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.158671 restraints weight = 83079.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.156831 restraints weight = 140080.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.153387 restraints weight = 115804.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152208 restraints weight = 126587.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.149786 restraints weight = 103237.703| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.7370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.224 44838 Z= 1.048 Angle : 1.439 24.122 61536 Z= 0.743 Chirality : 0.071 0.353 7949 Planarity : 0.008 0.131 8238 Dihedral : 7.064 85.812 7595 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.51 % Favored : 92.33 % Rotamer: Outliers : 7.81 % Allowed : 23.97 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.76 (0.10), residues: 7069 helix: 0.28 (0.07), residues: 4860 sheet: -2.12 (0.30), residues: 306 loop : -2.10 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG B2199 TYR 0.056 0.006 TYR C2568 PHE 0.083 0.006 PHE C2390 TRP 0.033 0.005 TRP B2204 HIS 0.035 0.005 HIS C2063 Details of bonding type rmsd covalent geometry : bond 0.02476 (44818) covalent geometry : angle 1.43428 (61524) SS BOND : bond 0.04911 ( 4) SS BOND : angle 3.87593 ( 8) hydrogen bonds : bond 0.06895 ( 3604) hydrogen bonds : angle 6.02222 (10551) metal coordination : bond 0.08283 ( 16) metal coordination : angle 13.92172 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 575 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2191 MET cc_start: 0.8053 (mmm) cc_final: 0.7653 (mtm) REVERT: C 1894 CYS cc_start: 0.6335 (p) cc_final: 0.4849 (t) REVERT: C 2150 GLU cc_start: 0.8707 (mp0) cc_final: 0.8450 (mp0) REVERT: D 1785 PHE cc_start: 0.7599 (t80) cc_final: 0.7232 (t80) REVERT: D 2033 TYR cc_start: 0.7625 (t80) cc_final: 0.7363 (t80) outliers start: 186 outliers final: 148 residues processed: 711 average time/residue: 0.2305 time to fit residues: 284.9416 Evaluate side-chains 689 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 541 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 THR Chi-restraints excluded: chain A residue 1744 THR Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1793 MET Chi-restraints excluded: chain A residue 1800 THR Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1888 LEU Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1928 TYR Chi-restraints excluded: chain A residue 1965 ASN Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 2061 SER Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2127 VAL Chi-restraints excluded: chain A residue 2158 THR Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2194 ILE Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2218 ILE Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2361 SER Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2455 CYS Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2525 SER Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain B residue 1734 THR Chi-restraints excluded: chain B residue 1740 LEU Chi-restraints excluded: chain B residue 1754 ILE Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1788 VAL Chi-restraints excluded: chain B residue 1904 VAL Chi-restraints excluded: chain B residue 1937 VAL Chi-restraints excluded: chain B residue 1952 CYS Chi-restraints excluded: chain B residue 1959 ILE Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2070 LEU Chi-restraints excluded: chain B residue 2121 THR Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2218 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2361 SER Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2455 CYS Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2503 ILE Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2556 GLU Chi-restraints excluded: chain C residue 1883 ASN Chi-restraints excluded: chain C residue 1897 ASN Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1952 CYS Chi-restraints excluded: chain C residue 1988 LEU Chi-restraints excluded: chain C residue 2001 LEU Chi-restraints excluded: chain C residue 2051 HIS Chi-restraints excluded: chain C residue 2055 ILE Chi-restraints excluded: chain C residue 2056 LEU Chi-restraints excluded: chain C residue 2058 LEU Chi-restraints excluded: chain C residue 2069 HIS Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2202 THR Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2290 LEU Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2301 VAL Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2329 THR Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2362 VAL Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2503 ILE Chi-restraints excluded: chain C residue 2509 LEU Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2525 SER Chi-restraints excluded: chain C residue 2573 VAL Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 1734 THR Chi-restraints excluded: chain D residue 1749 ILE Chi-restraints excluded: chain D residue 1765 ASN Chi-restraints excluded: chain D residue 1899 THR Chi-restraints excluded: chain D residue 1903 LEU Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1956 GLN Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2067 LEU Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2127 VAL Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2222 PHE Chi-restraints excluded: chain D residue 2282 LEU Chi-restraints excluded: chain D residue 2284 ILE Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2329 THR Chi-restraints excluded: chain D residue 2332 LEU Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2343 ILE Chi-restraints excluded: chain D residue 2353 GLU Chi-restraints excluded: chain D residue 2361 SER Chi-restraints excluded: chain D residue 2371 LEU Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2488 SER Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2507 ILE Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2523 LEU Chi-restraints excluded: chain D residue 2526 GLU Chi-restraints excluded: chain D residue 2531 GLU Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2549 ASP Chi-restraints excluded: chain D residue 2573 VAL Chi-restraints excluded: chain D residue 2575 VAL Chi-restraints excluded: chain D residue 2584 THR Chi-restraints excluded: chain D residue 2609 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 330 optimal weight: 0.6980 chunk 266 optimal weight: 50.0000 chunk 142 optimal weight: 0.8980 chunk 460 optimal weight: 40.0000 chunk 501 optimal weight: 0.9980 chunk 400 optimal weight: 50.0000 chunk 499 optimal weight: 1.9990 chunk 410 optimal weight: 50.0000 chunk 631 optimal weight: 50.0000 chunk 353 optimal weight: 0.9990 chunk 282 optimal weight: 50.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1774 ASN ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2210 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2472 ASN B1889 GLN ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2323 HIS C1871 GLN ** C1884 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1939 GLN ** C1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2135 GLN ** C2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1751 GLN D1773 HIS ** D1790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.203899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.168700 restraints weight = 84987.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.165342 restraints weight = 113781.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.163133 restraints weight = 78519.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.161900 restraints weight = 67774.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.160383 restraints weight = 60583.721| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.7069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 44838 Z= 0.143 Angle : 0.612 17.179 61536 Z= 0.316 Chirality : 0.040 0.267 7949 Planarity : 0.003 0.059 8238 Dihedral : 5.305 89.157 7595 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.27 % Allowed : 28.21 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.10), residues: 7069 helix: 1.77 (0.07), residues: 4875 sheet: -1.99 (0.30), residues: 308 loop : -1.59 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2524 TYR 0.052 0.002 TYR C2054 PHE 0.033 0.002 PHE B1910 TRP 0.023 0.002 TRP C2601 HIS 0.018 0.001 HIS C2051 Details of bonding type rmsd covalent geometry : bond 0.00321 (44818) covalent geometry : angle 0.60924 (61524) SS BOND : bond 0.00228 ( 4) SS BOND : angle 2.11027 ( 8) hydrogen bonds : bond 0.03259 ( 3604) hydrogen bonds : angle 4.01113 (10551) metal coordination : bond 0.00894 ( 16) metal coordination : angle 5.98869 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 622 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2191 MET cc_start: 0.7562 (mmm) cc_final: 0.6893 (mtm) REVERT: B 2400 ASP cc_start: 0.7564 (m-30) cc_final: 0.7348 (m-30) REVERT: C 1871 GLN cc_start: 0.5289 (mm110) cc_final: 0.5048 (mm-40) REVERT: C 2133 MET cc_start: 0.8507 (mmm) cc_final: 0.8116 (mmm) REVERT: C 2155 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9034 (mm) REVERT: C 2271 ARG cc_start: 0.7403 (tpt170) cc_final: 0.6174 (tpt90) REVERT: D 1727 ARG cc_start: 0.7932 (mmt180) cc_final: 0.7567 (tpp80) REVERT: D 1785 PHE cc_start: 0.7707 (t80) cc_final: 0.7331 (t80) REVERT: D 1870 MET cc_start: 0.7143 (tpp) cc_final: 0.6927 (tpt) REVERT: D 1960 VAL cc_start: 0.8107 (m) cc_final: 0.7858 (p) REVERT: D 2033 TYR cc_start: 0.7240 (t80) cc_final: 0.7029 (t80) REVERT: D 2063 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.6950 (t-90) outliers start: 78 outliers final: 58 residues processed: 673 average time/residue: 0.2233 time to fit residues: 259.4929 Evaluate side-chains 645 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 585 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 2061 SER Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2217 ILE Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2354 THR Chi-restraints excluded: chain A residue 2361 SER Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2062 ARG Chi-restraints excluded: chain B residue 2067 LEU Chi-restraints excluded: chain B residue 2070 LEU Chi-restraints excluded: chain B residue 2072 LYS Chi-restraints excluded: chain B residue 2121 THR Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2361 SER Chi-restraints excluded: chain B residue 2455 CYS Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain C residue 1952 CYS Chi-restraints excluded: chain C residue 2051 HIS Chi-restraints excluded: chain C residue 2055 ILE Chi-restraints excluded: chain C residue 2069 HIS Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2525 SER Chi-restraints excluded: chain C residue 2561 LEU Chi-restraints excluded: chain C residue 2581 THR Chi-restraints excluded: chain D residue 1900 ASN Chi-restraints excluded: chain D residue 1903 LEU Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1956 GLN Chi-restraints excluded: chain D residue 2063 HIS Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2361 SER Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2488 SER Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2575 VAL Chi-restraints excluded: chain D residue 2609 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 570 optimal weight: 50.0000 chunk 645 optimal weight: 50.0000 chunk 412 optimal weight: 50.0000 chunk 256 optimal weight: 50.0000 chunk 622 optimal weight: 50.0000 chunk 3 optimal weight: 50.0000 chunk 699 optimal weight: 0.5980 chunk 83 optimal weight: 50.0000 chunk 397 optimal weight: 50.0000 chunk 239 optimal weight: 50.0000 chunk 174 optimal weight: 0.6980 overall best weight: 30.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1773 HIS A1797 GLN A1976 ASN A2063 HIS ** A2064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2179 HIS ** A2210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2550 ASN ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1790 HIS ** B1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1883 ASN ** B1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1953 HIS ** C2063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2337 HIS D1773 HIS D1884 HIS ** D1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1900 ASN D2135 GLN ** D2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2337 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.179538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.143771 restraints weight = 85702.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.141284 restraints weight = 165172.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.135291 restraints weight = 125543.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134574 restraints weight = 133105.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133100 restraints weight = 106676.007| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.9461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.048 0.397 44838 Z= 2.027 Angle : 2.361 39.102 61536 Z= 1.225 Chirality : 0.128 0.880 7949 Planarity : 0.014 0.175 8238 Dihedral : 9.396 84.702 7595 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 37.66 Ramachandran Plot: Outliers : 0.85 % Allowed : 13.38 % Favored : 85.77 % Rotamer: Outliers : 6.34 % Allowed : 26.70 % Favored : 66.96 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.19 % 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: -3.80 (0.08), residues: 7069 helix: -2.05 (0.06), residues: 4767 sheet: -2.92 (0.34), residues: 187 loop : -3.20 (0.12), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.004 ARG D2524 TYR 0.117 0.011 TYR A2223 PHE 0.131 0.011 PHE A2539 TRP 0.071 0.010 TRP A2184 HIS 0.039 0.008 HIS C2337 Details of bonding type rmsd covalent geometry : bond 0.04796 (44818) covalent geometry : angle 2.35397 (61524) SS BOND : bond 0.09191 ( 4) SS BOND : angle 6.58897 ( 8) hydrogen bonds : bond 0.10816 ( 3604) hydrogen bonds : angle 8.72508 (10551) metal coordination : bond 0.16957 ( 16) metal coordination : angle 21.55882 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 561 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2271 ARG cc_start: 0.8463 (tpt170) cc_final: 0.7416 (ttt180) REVERT: A 2352 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8259 (mm-30) REVERT: B 2191 MET cc_start: 0.8316 (mmm) cc_final: 0.7854 (mtm) REVERT: C 1939 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: C 2030 LYS cc_start: 0.8436 (tptt) cc_final: 0.8102 (pttp) REVERT: C 2172 PHE cc_start: 0.8683 (t80) cc_final: 0.8269 (t80) REVERT: D 1762 ASP cc_start: 0.8249 (t0) cc_final: 0.8029 (t0) REVERT: D 1771 SER cc_start: 0.7940 (t) cc_final: 0.7703 (p) REVERT: D 1772 PHE cc_start: 0.7843 (m-80) cc_final: 0.7564 (m-80) REVERT: D 1785 PHE cc_start: 0.7936 (t80) cc_final: 0.7517 (t80) REVERT: D 1959 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8370 (mp) outliers start: 151 outliers final: 127 residues processed: 670 average time/residue: 0.2002 time to fit residues: 233.5593 Evaluate side-chains 678 residues out of total 6647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 549 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1800 THR Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1928 TYR Chi-restraints excluded: chain A residue 1965 ASN Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 2055 ILE Chi-restraints excluded: chain A residue 2061 SER Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2129 GLN Chi-restraints excluded: chain A residue 2148 THR Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2194 ILE Chi-restraints excluded: chain A residue 2218 ILE Chi-restraints excluded: chain A residue 2222 PHE Chi-restraints excluded: chain A residue 2265 ILE Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2284 ILE Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2361 SER Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2455 CYS Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain A residue 2600 ASP Chi-restraints excluded: chain B residue 1729 ASP Chi-restraints excluded: chain B residue 1734 THR Chi-restraints excluded: chain B residue 1754 ILE Chi-restraints excluded: chain B residue 1790 HIS Chi-restraints excluded: chain B residue 1904 VAL Chi-restraints excluded: chain B residue 1937 VAL Chi-restraints excluded: chain B residue 1952 CYS Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2063 HIS Chi-restraints excluded: chain B residue 2067 LEU Chi-restraints excluded: chain B residue 2070 LEU Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2269 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2294 ILE Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2324 VAL Chi-restraints excluded: chain B residue 2361 SER Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2525 SER Chi-restraints excluded: chain B residue 2593 MET Chi-restraints excluded: chain C residue 1883 ASN Chi-restraints excluded: chain C residue 1901 TYR Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1939 GLN Chi-restraints excluded: chain C residue 1952 CYS Chi-restraints excluded: chain C residue 1973 LEU Chi-restraints excluded: chain C residue 1988 LEU Chi-restraints excluded: chain C residue 2051 HIS Chi-restraints excluded: chain C residue 2055 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2177 PHE Chi-restraints excluded: chain C residue 2202 THR Chi-restraints excluded: chain C residue 2301 VAL Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2329 THR Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2362 VAL Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2503 ILE Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2525 SER Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain C residue 2561 LEU Chi-restraints excluded: chain C residue 2573 VAL Chi-restraints excluded: chain C residue 2581 THR Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain C residue 2594 ILE Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain C residue 2611 VAL Chi-restraints excluded: chain D residue 1724 THR Chi-restraints excluded: chain D residue 1734 THR Chi-restraints excluded: chain D residue 1894 CYS Chi-restraints excluded: chain D residue 1899 THR Chi-restraints excluded: chain D residue 1903 LEU Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1956 GLN Chi-restraints excluded: chain D residue 1959 ILE Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 2026 VAL Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2121 THR Chi-restraints excluded: chain D residue 2127 VAL Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2278 ILE Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2323 HIS Chi-restraints excluded: chain D residue 2324 VAL Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2343 ILE Chi-restraints excluded: chain D residue 2361 SER Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2488 SER Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2525 SER Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2549 ASP Chi-restraints excluded: chain D residue 2573 VAL Chi-restraints excluded: chain D residue 2575 VAL Chi-restraints excluded: chain D residue 2609 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 330 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 590 optimal weight: 50.0000 chunk 648 optimal weight: 50.0000 chunk 543 optimal weight: 30.0000 chunk 717 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 465 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 99 optimal weight: 40.0000 chunk 133 optimal weight: 3.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1976 ASN ** A2064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2210 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2550 ASN B1769 GLN B1790 HIS B1885 ASN ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1884 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1956 GLN ** C2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1773 HIS ** D1897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2550 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.200996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.170440 restraints weight = 80812.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.167388 restraints weight = 112056.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.164296 restraints weight = 97266.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.163068 restraints weight = 94822.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.161309 restraints weight = 79408.557| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.8815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 44838 Z= 0.238 Angle : 0.765 17.505 61536 Z= 0.396 Chirality : 0.044 0.297 7949 Planarity : 0.005 0.071 8238 Dihedral : 6.450 80.242 7595 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.80 % Favored : 94.19 % Rotamer: Outliers : 3.02 % Allowed : 30.48 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.20 (0.10), residues: 7069 helix: 0.05 (0.07), residues: 4853 sheet: -2.82 (0.33), residues: 216 loop : -2.52 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A2524 TYR 0.048 0.002 TYR C2054 PHE 0.059 0.003 PHE D1876 TRP 0.026 0.002 TRP D2601 HIS 0.019 0.002 HIS B1790 Details of bonding type rmsd covalent geometry : bond 0.00547 (44818) covalent geometry : angle 0.76249 (61524) SS BOND : bond 0.01129 ( 4) SS BOND : angle 2.47618 ( 8) hydrogen bonds : bond 0.04316 ( 3604) hydrogen bonds : angle 5.14875 (10551) metal coordination : bond 0.01802 ( 16) metal coordination : angle 6.38870 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9536.26 seconds wall clock time: 163 minutes 36.70 seconds (9816.70 seconds total)