Starting phenix.real_space_refine (version: dev) on Wed Dec 14 03:14:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3t_25670/12_2022/7t3t_25670_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3t_25670/12_2022/7t3t_25670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3t_25670/12_2022/7t3t_25670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3t_25670/12_2022/7t3t_25670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3t_25670/12_2022/7t3t_25670_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3t_25670/12_2022/7t3t_25670_updated.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.047 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 68516 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 17072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2121, 17072 Classifications: {'peptide': 2121} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 58, 'TRANS': 2062} Chain breaks: 22 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 17072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2121, 17072 Classifications: {'peptide': 2121} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 58, 'TRANS': 2062} Chain breaks: 22 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 17072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2121, 17072 Classifications: {'peptide': 2121} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 58, 'TRANS': 2062} Chain breaks: 22 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 17072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2121, 17072 Classifications: {'peptide': 2121} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 58, 'TRANS': 2062} Chain breaks: 22 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 38 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: 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: "C" 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: "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 16354 SG CYS A2538 97.503 133.497 102.719 1.00 82.09 S ATOM 16379 SG CYS A2541 99.288 131.890 99.791 1.00 68.73 S ATOM 33426 SG CYS B2538 104.962 97.515 102.718 1.00 87.51 S ATOM 33451 SG CYS B2541 106.569 99.300 99.790 1.00 72.72 S ATOM 50498 SG CYS C2538 140.956 104.966 102.714 1.00 84.57 S ATOM 50523 SG CYS C2541 139.171 106.573 99.786 1.00 70.64 S ATOM 67570 SG CYS D2538 133.495 140.961 102.719 1.00 84.82 S ATOM 67595 SG CYS D2541 131.888 139.176 99.791 1.00 72.14 S Time building chain proxies: 28.74, per 1000 atoms: 0.42 Number of scatterers: 68516 At special positions: 0 Unit cell: (239.292, 239.292, 180.504, 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 412 16.00 P 24 15.00 O 12664 8.00 N 11712 7.00 C 43696 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 - 3.50 Amino acid : False - 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: 23.67 Conformation dependent library (CDL) restraints added in 7.4 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 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 416 helices and 60 sheets defined 60.1% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.43 Creating SS restraints... Processing helix chain 'A' and resid 52 through 55 Processing helix chain 'A' and resid 66 through 75 Processing helix chain 'A' and resid 88 through 111 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 466 through 484 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 539 through 542 removed outlier: 3.910A pdb=" N SER A 542 " --> pdb=" O GLU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 539 through 542' Processing helix chain 'A' and resid 544 through 564 Proline residue: A 548 - end of helix Processing helix chain 'A' and resid 568 through 583 removed outlier: 4.271A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLY A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 removed outlier: 4.201A pdb=" N ASN A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 625 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 646 through 657 Processing helix chain 'A' and resid 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 720 through 739 removed outlier: 3.512A pdb=" N VAL A 725 " --> pdb=" O HIS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 754 removed outlier: 4.263A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 764 Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 812 through 819 Processing helix chain 'A' and resid 831 through 845 Processing helix chain 'A' and resid 856 through 873 Processing helix chain 'A' and resid 878 through 892 Processing helix chain 'A' and resid 963 through 997 Processing helix chain 'A' and resid 1026 through 1036 Processing helix chain 'A' and resid 1053 through 1064 Processing helix chain 'A' and resid 1068 through 1082 removed outlier: 3.838A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1094 Processing helix chain 'A' and resid 1101 through 1122 Processing helix chain 'A' and resid 1169 through 1183 Processing helix chain 'A' and resid 1187 through 1200 removed outlier: 4.269A pdb=" N LYS A1191 " --> pdb=" O GLU A1187 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS A1192 " --> pdb=" O GLN A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1211 Processing helix chain 'A' and resid 1219 through 1235 Processing helix chain 'A' and resid 1240 through 1247 Processing helix chain 'A' and resid 1250 through 1252 No H-bonds generated for 'chain 'A' and resid 1250 through 1252' Processing helix chain 'A' and resid 1259 through 1267 Processing helix chain 'A' and resid 1272 through 1276 Processing helix chain 'A' and resid 1280 through 1292 Processing helix chain 'A' and resid 1297 through 1306 Processing helix chain 'A' and resid 1315 through 1328 Processing helix chain 'A' and resid 1339 through 1352 removed outlier: 4.204A pdb=" N ALA A1351 " --> pdb=" O ASP A1347 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA A1352 " --> pdb=" O MET A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1377 removed outlier: 3.674A pdb=" N GLU A1377 " --> pdb=" O ALA A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1390 Processing helix chain 'A' and resid 1393 through 1401 Processing helix chain 'A' and resid 1407 through 1420 Processing helix chain 'A' and resid 1430 through 1433 Processing helix chain 'A' and resid 1436 through 1450 removed outlier: 3.688A pdb=" N ARG A1450 " --> pdb=" O LEU A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1481 removed outlier: 4.867A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1507 Processing helix chain 'A' and resid 1521 through 1533 removed outlier: 3.622A pdb=" N ARG A1527 " --> pdb=" O GLU A1523 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A1528 " --> pdb=" O ALA A1524 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A1532 " --> pdb=" O THR A1528 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A1533 " --> pdb=" O LEU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1622 Proline residue: A1608 - end of helix removed outlier: 4.165A pdb=" N GLN A1611 " --> pdb=" O LYS A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1640 Processing helix chain 'A' and resid 1642 through 1653 Processing helix chain 'A' and resid 1659 through 1673 Processing helix chain 'A' and resid 1684 through 1694 Processing helix chain 'A' and resid 1720 through 1731 Processing helix chain 'A' and resid 1733 through 1742 Processing helix chain 'A' and resid 1747 through 1761 Processing helix chain 'A' and resid 1766 through 1777 Processing helix chain 'A' and resid 1780 through 1802 removed outlier: 3.986A pdb=" N GLU A1783 " --> pdb=" O LYS A1780 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A1786 " --> pdb=" O GLU A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1880 Proline residue: A1872 - end of helix Processing helix chain 'A' and resid 1882 through 1884 No H-bonds generated for 'chain 'A' and resid 1882 through 1884' Processing helix chain 'A' and resid 1886 through 1894 removed outlier: 4.257A pdb=" N ARG A1893 " --> pdb=" O GLN A1889 " (cutoff:3.500A) Processing helix chain 'A' and resid 1903 through 1915 Processing helix chain 'A' and resid 1917 through 1921 Processing helix chain 'A' and resid 1934 through 1947 Processing helix chain 'A' and resid 1953 through 1960 Processing helix chain 'A' and resid 1966 through 1975 removed outlier: 3.582A pdb=" N ILE A1970 " --> pdb=" O GLY A1966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1979 through 1984 removed outlier: 4.654A pdb=" N LYS A1983 " --> pdb=" O SER A1979 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR A1984 " --> pdb=" O PRO A1980 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1979 through 1984' Processing helix chain 'A' and resid 1986 through 2003 Processing helix chain 'A' and resid 2011 through 2019 removed outlier: 4.220A pdb=" N ILE A2016 " --> pdb=" O ASN A2012 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A2019 " --> pdb=" O ARG A2015 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2034 Processing helix chain 'A' and resid 2046 through 2063 removed outlier: 4.090A pdb=" N ARG A2062 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS A2063 " --> pdb=" O GLN A2059 " (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 2142 through 2145 Processing helix chain 'A' and resid 2149 through 2158 Processing helix chain 'A' and resid 2168 through 2190 removed outlier: 4.242A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A2190 " --> pdb=" O ARG A2186 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2198 Processing helix chain 'A' and resid 2201 through 2221 Processing helix chain 'A' and resid 2266 through 2276 Processing helix chain 'A' and resid 2279 through 2304 removed outlier: 4.136A pdb=" N LEU A2282 " --> pdb=" O GLY A2279 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG A2304 " --> pdb=" O VAL A2301 " (cutoff:3.500A) Processing helix chain 'A' and resid 2320 through 2335 removed outlier: 3.584A pdb=" N TYR A2326 " --> pdb=" O TYR A2322 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A2327 " --> pdb=" O HIS A2323 " (cutoff:3.500A) Processing helix chain 'A' and resid 2341 through 2351 removed outlier: 4.439A pdb=" N PHE A2346 " --> pdb=" O SER A2342 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP A2347 " --> pdb=" O ILE A2343 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A2349 " --> pdb=" O LEU A2345 " (cutoff:3.500A) Processing helix chain 'A' and resid 2353 through 2364 Processing helix chain 'A' and resid 2366 through 2388 Processing helix chain 'A' and resid 2392 through 2394 No H-bonds generated for 'chain 'A' and resid 2392 through 2394' Processing helix chain 'A' and resid 2458 through 2468 Processing helix chain 'A' and resid 2476 through 2478 No H-bonds generated for 'chain 'A' and resid 2476 through 2478' Processing helix chain 'A' and resid 2490 through 2503 Processing helix chain 'A' and resid 2508 through 2513 Processing helix chain 'A' and resid 2515 through 2536 Processing helix chain 'A' and resid 2545 through 2548 Processing helix chain 'A' and resid 2555 through 2561 Processing helix chain 'A' and resid 2565 through 2577 Processing helix chain 'A' and resid 2580 through 2582 No H-bonds generated for 'chain 'A' and resid 2580 through 2582' Processing helix chain 'A' and resid 2585 through 2595 Processing helix chain 'A' and resid 2629 through 2645 removed outlier: 3.623A pdb=" N UNK A2633 " --> pdb=" O UNK A2629 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK A2636 " --> pdb=" O UNK A2632 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N UNK A2643 " --> pdb=" O UNK A2639 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 55 Processing helix chain 'B' and resid 66 through 75 Processing helix chain 'B' and resid 88 through 111 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 466 through 484 Processing helix chain 'B' and resid 493 through 495 No H-bonds generated for 'chain 'B' and resid 493 through 495' Processing helix chain 'B' and resid 503 through 512 Processing helix chain 'B' and resid 514 through 524 Processing helix chain 'B' and resid 539 through 542 removed outlier: 3.910A pdb=" N SER B 542 " --> pdb=" O GLU B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 539 through 542' Processing helix chain 'B' and resid 544 through 564 Proline residue: B 548 - end of helix Processing helix chain 'B' and resid 568 through 583 removed outlier: 4.271A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLY B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 601 removed outlier: 4.201A pdb=" N ASN B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 612 through 625 Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 646 through 657 Processing helix chain 'B' and resid 659 through 661 No H-bonds generated for 'chain 'B' and resid 659 through 661' Processing helix chain 'B' and resid 708 through 717 Processing helix chain 'B' and resid 720 through 739 removed outlier: 3.512A pdb=" N VAL B 725 " --> pdb=" O HIS B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 754 removed outlier: 4.263A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 764 Processing helix chain 'B' and resid 771 through 784 Processing helix chain 'B' and resid 812 through 819 Processing helix chain 'B' and resid 831 through 845 Processing helix chain 'B' and resid 856 through 873 Processing helix chain 'B' and resid 878 through 892 Processing helix chain 'B' and resid 963 through 997 Processing helix chain 'B' and resid 1026 through 1036 Processing helix chain 'B' and resid 1053 through 1064 Processing helix chain 'B' and resid 1068 through 1082 removed outlier: 3.838A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1094 Processing helix chain 'B' and resid 1101 through 1122 Processing helix chain 'B' and resid 1169 through 1183 Processing helix chain 'B' and resid 1187 through 1200 removed outlier: 4.269A pdb=" N LYS B1191 " --> pdb=" O GLU B1187 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS B1192 " --> pdb=" O GLN B1188 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1211 Processing helix chain 'B' and resid 1219 through 1235 Processing helix chain 'B' and resid 1240 through 1247 Processing helix chain 'B' and resid 1250 through 1252 No H-bonds generated for 'chain 'B' and resid 1250 through 1252' Processing helix chain 'B' and resid 1259 through 1267 Processing helix chain 'B' and resid 1272 through 1276 Processing helix chain 'B' and resid 1280 through 1292 Processing helix chain 'B' and resid 1297 through 1306 Processing helix chain 'B' and resid 1315 through 1328 Processing helix chain 'B' and resid 1339 through 1352 removed outlier: 4.203A pdb=" N ALA B1351 " --> pdb=" O ASP B1347 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA B1352 " --> pdb=" O MET B1348 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1377 removed outlier: 3.674A pdb=" N GLU B1377 " --> pdb=" O ALA B1373 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1390 Processing helix chain 'B' and resid 1393 through 1401 Processing helix chain 'B' and resid 1407 through 1420 Processing helix chain 'B' and resid 1430 through 1433 Processing helix chain 'B' and resid 1436 through 1450 removed outlier: 3.688A pdb=" N ARG B1450 " --> pdb=" O LEU B1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 1463 through 1481 removed outlier: 4.867A pdb=" N LEU B1473 " --> pdb=" O LEU B1469 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP B1474 " --> pdb=" O SER B1470 " (cutoff:3.500A) Processing helix chain 'B' and resid 1494 through 1507 Processing helix chain 'B' and resid 1521 through 1533 removed outlier: 3.622A pdb=" N ARG B1527 " --> pdb=" O GLU B1523 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B1528 " --> pdb=" O ALA B1524 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B1532 " --> pdb=" O THR B1528 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA B1533 " --> pdb=" O LEU B1529 " (cutoff:3.500A) Processing helix chain 'B' and resid 1590 through 1622 Proline residue: B1608 - end of helix removed outlier: 4.165A pdb=" N GLN B1611 " --> pdb=" O LYS B1607 " (cutoff:3.500A) Processing helix chain 'B' and resid 1635 through 1640 Processing helix chain 'B' and resid 1642 through 1653 Processing helix chain 'B' and resid 1659 through 1673 Processing helix chain 'B' and resid 1684 through 1694 Processing helix chain 'B' and resid 1720 through 1731 Processing helix chain 'B' and resid 1733 through 1742 Processing helix chain 'B' and resid 1747 through 1761 Processing helix chain 'B' and resid 1766 through 1777 Processing helix chain 'B' and resid 1780 through 1802 removed outlier: 3.986A pdb=" N GLU B1783 " --> pdb=" O LYS B1780 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B1786 " --> pdb=" O GLU B1783 " (cutoff:3.500A) Processing helix chain 'B' and resid 1868 through 1880 Proline residue: B1872 - end of helix Processing helix chain 'B' and resid 1882 through 1884 No H-bonds generated for 'chain 'B' and resid 1882 through 1884' Processing helix chain 'B' and resid 1886 through 1894 removed outlier: 4.257A pdb=" N ARG B1893 " --> pdb=" O GLN B1889 " (cutoff:3.500A) Processing helix chain 'B' and resid 1903 through 1915 Processing helix chain 'B' and resid 1917 through 1921 Processing helix chain 'B' and resid 1934 through 1947 Processing helix chain 'B' and resid 1953 through 1960 Processing helix chain 'B' and resid 1966 through 1975 removed outlier: 3.582A pdb=" N ILE B1970 " --> pdb=" O GLY B1966 " (cutoff:3.500A) Processing helix chain 'B' and resid 1979 through 1984 removed outlier: 4.654A pdb=" N LYS B1983 " --> pdb=" O SER B1979 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1979 through 1984' Processing helix chain 'B' and resid 1986 through 2003 Processing helix chain 'B' and resid 2011 through 2019 removed outlier: 4.220A pdb=" N ILE B2016 " --> pdb=" O ASN B2012 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B2019 " --> pdb=" O ARG B2015 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2034 Processing helix chain 'B' and resid 2046 through 2063 removed outlier: 4.089A pdb=" N ARG B2062 " --> pdb=" O LEU B2058 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS B2063 " --> pdb=" O GLN B2059 " (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 2142 through 2145 Processing helix chain 'B' and resid 2149 through 2158 Processing helix chain 'B' and resid 2168 through 2190 removed outlier: 4.242A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B2190 " --> pdb=" O ARG B2186 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2198 Processing helix chain 'B' and resid 2201 through 2221 Processing helix chain 'B' and resid 2266 through 2276 Processing helix chain 'B' and resid 2279 through 2304 removed outlier: 4.136A pdb=" N LEU B2282 " --> pdb=" O GLY B2279 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG B2304 " --> pdb=" O VAL B2301 " (cutoff:3.500A) Processing helix chain 'B' and resid 2320 through 2335 removed outlier: 3.584A pdb=" N TYR B2326 " --> pdb=" O TYR B2322 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B2327 " --> pdb=" O HIS B2323 " (cutoff:3.500A) Processing helix chain 'B' and resid 2341 through 2351 removed outlier: 4.439A pdb=" N PHE B2346 " --> pdb=" O SER B2342 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP B2347 " --> pdb=" O ILE B2343 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU B2348 " --> pdb=" O LEU B2344 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B2349 " --> pdb=" O LEU B2345 " (cutoff:3.500A) Processing helix chain 'B' and resid 2353 through 2364 Processing helix chain 'B' and resid 2366 through 2388 Processing helix chain 'B' and resid 2392 through 2394 No H-bonds generated for 'chain 'B' and resid 2392 through 2394' Processing helix chain 'B' and resid 2458 through 2468 Processing helix chain 'B' and resid 2476 through 2478 No H-bonds generated for 'chain 'B' and resid 2476 through 2478' Processing helix chain 'B' and resid 2490 through 2503 Processing helix chain 'B' and resid 2508 through 2513 Processing helix chain 'B' and resid 2515 through 2536 Processing helix chain 'B' and resid 2545 through 2548 Processing helix chain 'B' and resid 2555 through 2561 Processing helix chain 'B' and resid 2565 through 2577 Processing helix chain 'B' and resid 2580 through 2582 No H-bonds generated for 'chain 'B' and resid 2580 through 2582' Processing helix chain 'B' and resid 2585 through 2595 Processing helix chain 'B' and resid 2629 through 2645 removed outlier: 3.623A pdb=" N UNK B2633 " --> pdb=" O UNK B2629 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK B2636 " --> pdb=" O UNK B2632 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N UNK B2643 " --> pdb=" O UNK B2639 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 55 Processing helix chain 'C' and resid 66 through 75 Processing helix chain 'C' and resid 88 through 111 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 466 through 484 Processing helix chain 'C' and resid 493 through 495 No H-bonds generated for 'chain 'C' and resid 493 through 495' Processing helix chain 'C' and resid 503 through 512 Processing helix chain 'C' and resid 514 through 524 Processing helix chain 'C' and resid 539 through 542 removed outlier: 3.910A pdb=" N SER C 542 " --> pdb=" O GLU C 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 539 through 542' Processing helix chain 'C' and resid 544 through 564 Proline residue: C 548 - end of helix Processing helix chain 'C' and resid 568 through 583 removed outlier: 4.272A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY C 579 " --> pdb=" O ALA C 575 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET C 580 " --> pdb=" O LYS C 576 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 601 removed outlier: 4.201A pdb=" N ASN C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 609 Processing helix chain 'C' and resid 612 through 625 Processing helix chain 'C' and resid 628 through 637 Processing helix chain 'C' and resid 646 through 657 Processing helix chain 'C' and resid 659 through 661 No H-bonds generated for 'chain 'C' and resid 659 through 661' Processing helix chain 'C' and resid 708 through 717 Processing helix chain 'C' and resid 720 through 739 removed outlier: 3.512A pdb=" N VAL C 725 " --> pdb=" O HIS C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 754 removed outlier: 4.263A pdb=" N GLU C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 764 Processing helix chain 'C' and resid 771 through 784 Processing helix chain 'C' and resid 812 through 819 Processing helix chain 'C' and resid 831 through 845 Processing helix chain 'C' and resid 856 through 873 Processing helix chain 'C' and resid 878 through 892 Processing helix chain 'C' and resid 963 through 997 Processing helix chain 'C' and resid 1026 through 1036 Processing helix chain 'C' and resid 1053 through 1064 Processing helix chain 'C' and resid 1068 through 1082 removed outlier: 3.838A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) Processing helix chain 'C' and resid 1084 through 1094 Processing helix chain 'C' and resid 1101 through 1122 Processing helix chain 'C' and resid 1169 through 1183 Processing helix chain 'C' and resid 1187 through 1200 removed outlier: 4.269A pdb=" N LYS C1191 " --> pdb=" O GLU C1187 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS C1192 " --> pdb=" O GLN C1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1211 Processing helix chain 'C' and resid 1219 through 1235 Processing helix chain 'C' and resid 1240 through 1247 Processing helix chain 'C' and resid 1250 through 1252 No H-bonds generated for 'chain 'C' and resid 1250 through 1252' Processing helix chain 'C' and resid 1259 through 1267 Processing helix chain 'C' and resid 1272 through 1276 Processing helix chain 'C' and resid 1280 through 1292 Processing helix chain 'C' and resid 1297 through 1306 Processing helix chain 'C' and resid 1315 through 1328 Processing helix chain 'C' and resid 1339 through 1352 removed outlier: 4.204A pdb=" N ALA C1351 " --> pdb=" O ASP C1347 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C1352 " --> pdb=" O MET C1348 " (cutoff:3.500A) Processing helix chain 'C' and resid 1361 through 1377 removed outlier: 3.674A pdb=" N GLU C1377 " --> pdb=" O ALA C1373 " (cutoff:3.500A) Processing helix chain 'C' and resid 1381 through 1390 Processing helix chain 'C' and resid 1393 through 1401 Processing helix chain 'C' and resid 1407 through 1420 Processing helix chain 'C' and resid 1430 through 1433 Processing helix chain 'C' and resid 1436 through 1450 removed outlier: 3.688A pdb=" N ARG C1450 " --> pdb=" O LEU C1446 " (cutoff:3.500A) Processing helix chain 'C' and resid 1463 through 1481 removed outlier: 4.867A pdb=" N LEU C1473 " --> pdb=" O LEU C1469 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP C1474 " --> pdb=" O SER C1470 " (cutoff:3.500A) Processing helix chain 'C' and resid 1494 through 1507 Processing helix chain 'C' and resid 1521 through 1533 removed outlier: 3.622A pdb=" N ARG C1527 " --> pdb=" O GLU C1523 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C1528 " --> pdb=" O ALA C1524 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C1532 " --> pdb=" O THR C1528 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA C1533 " --> pdb=" O LEU C1529 " (cutoff:3.500A) Processing helix chain 'C' and resid 1590 through 1622 Proline residue: C1608 - end of helix removed outlier: 4.165A pdb=" N GLN C1611 " --> pdb=" O LYS C1607 " (cutoff:3.500A) Processing helix chain 'C' and resid 1635 through 1640 Processing helix chain 'C' and resid 1642 through 1653 Processing helix chain 'C' and resid 1659 through 1673 Processing helix chain 'C' and resid 1684 through 1694 Processing helix chain 'C' and resid 1720 through 1731 Processing helix chain 'C' and resid 1733 through 1742 Processing helix chain 'C' and resid 1747 through 1761 Processing helix chain 'C' and resid 1766 through 1777 Processing helix chain 'C' and resid 1780 through 1802 removed outlier: 3.986A pdb=" N GLU C1783 " --> pdb=" O LYS C1780 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C1786 " --> pdb=" O GLU C1783 " (cutoff:3.500A) Processing helix chain 'C' and resid 1868 through 1880 Proline residue: C1872 - end of helix Processing helix chain 'C' and resid 1882 through 1884 No H-bonds generated for 'chain 'C' and resid 1882 through 1884' Processing helix chain 'C' and resid 1886 through 1894 removed outlier: 4.257A pdb=" N ARG C1893 " --> pdb=" O GLN C1889 " (cutoff:3.500A) Processing helix chain 'C' and resid 1903 through 1915 Processing helix chain 'C' and resid 1917 through 1921 Processing helix chain 'C' and resid 1934 through 1947 Processing helix chain 'C' and resid 1953 through 1960 Processing helix chain 'C' and resid 1966 through 1975 removed outlier: 3.582A pdb=" N ILE C1970 " --> pdb=" O GLY C1966 " (cutoff:3.500A) Processing helix chain 'C' and resid 1979 through 1984 removed outlier: 4.653A pdb=" N LYS C1983 " --> pdb=" O SER C1979 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1979 through 1984' Processing helix chain 'C' and resid 1986 through 2003 Processing helix chain 'C' and resid 2011 through 2019 removed outlier: 4.220A pdb=" N ILE C2016 " --> pdb=" O ASN C2012 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C2019 " --> pdb=" O ARG C2015 " (cutoff:3.500A) Processing helix chain 'C' and resid 2022 through 2034 Processing helix chain 'C' and resid 2046 through 2063 removed outlier: 4.090A pdb=" N ARG C2062 " --> pdb=" O LEU C2058 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N HIS C2063 " --> pdb=" O GLN C2059 " (cutoff:3.500A) Processing helix chain 'C' and resid 2065 through 2071 Processing helix chain 'C' and resid 2113 through 2119 Processing helix chain 'C' and resid 2142 through 2145 Processing helix chain 'C' and resid 2149 through 2158 Processing helix chain 'C' and resid 2168 through 2190 removed outlier: 4.242A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER C2190 " --> pdb=" O ARG C2186 " (cutoff:3.500A) Processing helix chain 'C' and resid 2194 through 2198 Processing helix chain 'C' and resid 2201 through 2221 Processing helix chain 'C' and resid 2266 through 2276 Processing helix chain 'C' and resid 2279 through 2304 removed outlier: 4.136A pdb=" N LEU C2282 " --> pdb=" O GLY C2279 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG C2304 " --> pdb=" O VAL C2301 " (cutoff:3.500A) Processing helix chain 'C' and resid 2320 through 2335 removed outlier: 3.584A pdb=" N TYR C2326 " --> pdb=" O TYR C2322 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C2327 " --> pdb=" O HIS C2323 " (cutoff:3.500A) Processing helix chain 'C' and resid 2341 through 2351 removed outlier: 4.439A pdb=" N PHE C2346 " --> pdb=" O SER C2342 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP C2347 " --> pdb=" O ILE C2343 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU C2348 " --> pdb=" O LEU C2344 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C2349 " --> pdb=" O LEU C2345 " (cutoff:3.500A) Processing helix chain 'C' and resid 2353 through 2364 Processing helix chain 'C' and resid 2366 through 2388 Processing helix chain 'C' and resid 2392 through 2394 No H-bonds generated for 'chain 'C' and resid 2392 through 2394' Processing helix chain 'C' and resid 2458 through 2468 Processing helix chain 'C' and resid 2476 through 2478 No H-bonds generated for 'chain 'C' and resid 2476 through 2478' Processing helix chain 'C' and resid 2490 through 2503 Processing helix chain 'C' and resid 2508 through 2513 Processing helix chain 'C' and resid 2515 through 2536 Processing helix chain 'C' and resid 2545 through 2548 Processing helix chain 'C' and resid 2555 through 2561 Processing helix chain 'C' and resid 2565 through 2577 Processing helix chain 'C' and resid 2580 through 2582 No H-bonds generated for 'chain 'C' and resid 2580 through 2582' Processing helix chain 'C' and resid 2585 through 2595 Processing helix chain 'C' and resid 2629 through 2645 removed outlier: 3.623A pdb=" N UNK C2633 " --> pdb=" O UNK C2629 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK C2636 " --> pdb=" O UNK C2632 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N UNK C2643 " --> pdb=" O UNK C2639 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 55 Processing helix chain 'D' and resid 66 through 75 Processing helix chain 'D' and resid 88 through 111 Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 273 through 275 No H-bonds generated for 'chain 'D' and resid 273 through 275' Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 466 through 484 Processing helix chain 'D' and resid 493 through 495 No H-bonds generated for 'chain 'D' and resid 493 through 495' Processing helix chain 'D' and resid 503 through 512 Processing helix chain 'D' and resid 514 through 524 Processing helix chain 'D' and resid 539 through 542 removed outlier: 3.910A pdb=" N SER D 542 " --> pdb=" O GLU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 539 through 542' Processing helix chain 'D' and resid 544 through 564 Proline residue: D 548 - end of helix Processing helix chain 'D' and resid 568 through 583 removed outlier: 4.271A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLY D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 601 removed outlier: 4.201A pdb=" N ASN D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 609 Processing helix chain 'D' and resid 612 through 625 Processing helix chain 'D' and resid 628 through 637 Processing helix chain 'D' and resid 646 through 657 Processing helix chain 'D' and resid 659 through 661 No H-bonds generated for 'chain 'D' and resid 659 through 661' Processing helix chain 'D' and resid 708 through 717 Processing helix chain 'D' and resid 720 through 739 removed outlier: 3.512A pdb=" N VAL D 725 " --> pdb=" O HIS D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 754 removed outlier: 4.263A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 764 Processing helix chain 'D' and resid 771 through 784 Processing helix chain 'D' and resid 812 through 819 Processing helix chain 'D' and resid 831 through 845 Processing helix chain 'D' and resid 856 through 873 Processing helix chain 'D' and resid 878 through 892 Processing helix chain 'D' and resid 963 through 997 Processing helix chain 'D' and resid 1026 through 1036 Processing helix chain 'D' and resid 1053 through 1064 Processing helix chain 'D' and resid 1068 through 1082 removed outlier: 3.839A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1094 Processing helix chain 'D' and resid 1101 through 1122 Processing helix chain 'D' and resid 1169 through 1183 Processing helix chain 'D' and resid 1187 through 1200 removed outlier: 4.269A pdb=" N LYS D1191 " --> pdb=" O GLU D1187 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS D1192 " --> pdb=" O GLN D1188 " (cutoff:3.500A) Processing helix chain 'D' and resid 1202 through 1211 Processing helix chain 'D' and resid 1219 through 1235 Processing helix chain 'D' and resid 1240 through 1247 Processing helix chain 'D' and resid 1250 through 1252 No H-bonds generated for 'chain 'D' and resid 1250 through 1252' Processing helix chain 'D' and resid 1259 through 1267 Processing helix chain 'D' and resid 1272 through 1276 Processing helix chain 'D' and resid 1280 through 1292 Processing helix chain 'D' and resid 1297 through 1306 Processing helix chain 'D' and resid 1315 through 1328 Processing helix chain 'D' and resid 1339 through 1352 removed outlier: 4.204A pdb=" N ALA D1351 " --> pdb=" O ASP D1347 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA D1352 " --> pdb=" O MET D1348 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1377 removed outlier: 3.674A pdb=" N GLU D1377 " --> pdb=" O ALA D1373 " (cutoff:3.500A) Processing helix chain 'D' and resid 1381 through 1390 Processing helix chain 'D' and resid 1393 through 1401 Processing helix chain 'D' and resid 1407 through 1420 Processing helix chain 'D' and resid 1430 through 1433 Processing helix chain 'D' and resid 1436 through 1450 removed outlier: 3.688A pdb=" N ARG D1450 " --> pdb=" O LEU D1446 " (cutoff:3.500A) Processing helix chain 'D' and resid 1463 through 1481 removed outlier: 4.867A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP D1474 " --> pdb=" O SER D1470 " (cutoff:3.500A) Processing helix chain 'D' and resid 1494 through 1507 Processing helix chain 'D' and resid 1521 through 1533 removed outlier: 3.622A pdb=" N ARG D1527 " --> pdb=" O GLU D1523 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR D1528 " --> pdb=" O ALA D1524 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D1532 " --> pdb=" O THR D1528 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA D1533 " --> pdb=" O LEU D1529 " (cutoff:3.500A) Processing helix chain 'D' and resid 1590 through 1622 Proline residue: D1608 - end of helix removed outlier: 4.164A pdb=" N GLN D1611 " --> pdb=" O LYS D1607 " (cutoff:3.500A) Processing helix chain 'D' and resid 1635 through 1640 Processing helix chain 'D' and resid 1642 through 1653 Processing helix chain 'D' and resid 1659 through 1673 Processing helix chain 'D' and resid 1684 through 1694 Processing helix chain 'D' and resid 1720 through 1731 Processing helix chain 'D' and resid 1733 through 1742 Processing helix chain 'D' and resid 1747 through 1761 Processing helix chain 'D' and resid 1766 through 1777 Processing helix chain 'D' and resid 1780 through 1802 removed outlier: 3.986A pdb=" N GLU D1783 " --> pdb=" O LYS D1780 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D1786 " --> pdb=" O GLU D1783 " (cutoff:3.500A) Processing helix chain 'D' and resid 1868 through 1880 Proline residue: D1872 - end of helix Processing helix chain 'D' and resid 1882 through 1884 No H-bonds generated for 'chain 'D' and resid 1882 through 1884' Processing helix chain 'D' and resid 1886 through 1894 removed outlier: 4.257A pdb=" N ARG D1893 " --> pdb=" O GLN D1889 " (cutoff:3.500A) Processing helix chain 'D' and resid 1903 through 1915 Processing helix chain 'D' and resid 1917 through 1921 Processing helix chain 'D' and resid 1934 through 1947 Processing helix chain 'D' and resid 1953 through 1960 Processing helix chain 'D' and resid 1966 through 1975 removed outlier: 3.582A pdb=" N ILE D1970 " --> pdb=" O GLY D1966 " (cutoff:3.500A) Processing helix chain 'D' and resid 1979 through 1984 removed outlier: 4.654A pdb=" N LYS D1983 " --> pdb=" O SER D1979 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR D1984 " --> pdb=" O PRO D1980 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1979 through 1984' Processing helix chain 'D' and resid 1986 through 2003 Processing helix chain 'D' and resid 2011 through 2019 removed outlier: 4.220A pdb=" N ILE D2016 " --> pdb=" O ASN D2012 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D2019 " --> pdb=" O ARG D2015 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2034 Processing helix chain 'D' and resid 2046 through 2063 removed outlier: 4.090A pdb=" N ARG D2062 " --> pdb=" O LEU D2058 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS D2063 " --> pdb=" O GLN D2059 " (cutoff:3.500A) Processing helix chain 'D' and resid 2065 through 2071 Processing helix chain 'D' and resid 2113 through 2119 Processing helix chain 'D' and resid 2142 through 2145 Processing helix chain 'D' and resid 2149 through 2158 Processing helix chain 'D' and resid 2168 through 2190 removed outlier: 4.243A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER D2190 " --> pdb=" O ARG D2186 " (cutoff:3.500A) Processing helix chain 'D' and resid 2194 through 2198 Processing helix chain 'D' and resid 2201 through 2221 Processing helix chain 'D' and resid 2266 through 2276 Processing helix chain 'D' and resid 2279 through 2304 removed outlier: 4.136A pdb=" N LEU D2282 " --> pdb=" O GLY D2279 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG D2304 " --> pdb=" O VAL D2301 " (cutoff:3.500A) Processing helix chain 'D' and resid 2320 through 2335 removed outlier: 3.584A pdb=" N TYR D2326 " --> pdb=" O TYR D2322 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D2327 " --> pdb=" O HIS D2323 " (cutoff:3.500A) Processing helix chain 'D' and resid 2341 through 2351 removed outlier: 4.439A pdb=" N PHE D2346 " --> pdb=" O SER D2342 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP D2347 " --> pdb=" O ILE D2343 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU D2348 " --> pdb=" O LEU D2344 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D2349 " --> pdb=" O LEU D2345 " (cutoff:3.500A) Processing helix chain 'D' and resid 2353 through 2364 Processing helix chain 'D' and resid 2366 through 2388 Processing helix chain 'D' and resid 2392 through 2394 No H-bonds generated for 'chain 'D' and resid 2392 through 2394' Processing helix chain 'D' and resid 2458 through 2468 Processing helix chain 'D' and resid 2476 through 2478 No H-bonds generated for 'chain 'D' and resid 2476 through 2478' Processing helix chain 'D' and resid 2490 through 2503 Processing helix chain 'D' and resid 2508 through 2513 Processing helix chain 'D' and resid 2515 through 2536 Processing helix chain 'D' and resid 2545 through 2548 Processing helix chain 'D' and resid 2555 through 2561 Processing helix chain 'D' and resid 2565 through 2577 Processing helix chain 'D' and resid 2580 through 2582 No H-bonds generated for 'chain 'D' and resid 2580 through 2582' Processing helix chain 'D' and resid 2585 through 2595 Processing helix chain 'D' and resid 2629 through 2645 removed outlier: 3.622A pdb=" N UNK D2633 " --> pdb=" O UNK D2629 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK D2636 " --> pdb=" O UNK D2632 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N UNK D2643 " --> pdb=" O UNK D2639 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 57 through 60 Processing sheet with id= B, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.786A pdb=" N SER A 120 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 194 through 196 Processing sheet with id= D, first strand: chain 'A' and resid 242 through 245 Processing sheet with id= E, first strand: chain 'A' and resid 252 through 257 Processing sheet with id= F, first strand: chain 'A' and resid 283 through 287 Processing sheet with id= G, first strand: chain 'A' and resid 314 through 319 Processing sheet with id= H, first strand: chain 'A' and resid 369 through 371 Processing sheet with id= I, first strand: chain 'A' and resid 397 through 400 Processing sheet with id= J, first strand: chain 'A' and resid 667 through 670 Processing sheet with id= K, first strand: chain 'A' and resid 800 through 802 removed outlier: 6.298A pdb=" N GLN A1096 " --> pdb=" O ARG A 801 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 2121 through 2127 Processing sheet with id= M, first strand: chain 'A' and resid 2396 through 2398 Processing sheet with id= N, first strand: chain 'A' and resid 13 through 18 removed outlier: 6.264A pdb=" N SER A 15 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 223 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TYR A 17 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE A 221 " --> pdb=" O TYR A 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 132 through 140 removed outlier: 3.733A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= Q, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.786A pdb=" N SER B 120 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 194 through 196 Processing sheet with id= S, first strand: chain 'B' and resid 242 through 245 Processing sheet with id= T, first strand: chain 'B' and resid 252 through 257 Processing sheet with id= U, first strand: chain 'B' and resid 283 through 287 Processing sheet with id= V, first strand: chain 'B' and resid 314 through 319 Processing sheet with id= W, first strand: chain 'B' and resid 369 through 371 Processing sheet with id= X, first strand: chain 'B' and resid 397 through 400 Processing sheet with id= Y, first strand: chain 'B' and resid 667 through 670 Processing sheet with id= Z, first strand: chain 'B' and resid 800 through 802 removed outlier: 6.298A pdb=" N GLN B1096 " --> pdb=" O ARG B 801 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'B' and resid 2121 through 2127 Processing sheet with id= AB, first strand: chain 'B' and resid 2396 through 2398 Processing sheet with id= AC, first strand: chain 'B' and resid 13 through 18 removed outlier: 6.264A pdb=" N SER B 15 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU B 223 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TYR B 17 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE B 221 " --> pdb=" O TYR B 17 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 132 through 140 removed outlier: 3.733A pdb=" N ARG B 149 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= AF, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.786A pdb=" N SER C 120 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 194 through 196 Processing sheet with id= AH, first strand: chain 'C' and resid 242 through 245 Processing sheet with id= AI, first strand: chain 'C' and resid 252 through 257 Processing sheet with id= AJ, first strand: chain 'C' and resid 283 through 287 Processing sheet with id= AK, first strand: chain 'C' and resid 314 through 319 Processing sheet with id= AL, first strand: chain 'C' and resid 369 through 371 Processing sheet with id= AM, first strand: chain 'C' and resid 397 through 400 Processing sheet with id= AN, first strand: chain 'C' and resid 667 through 670 Processing sheet with id= AO, first strand: chain 'C' and resid 800 through 802 removed outlier: 6.298A pdb=" N GLN C1096 " --> pdb=" O ARG C 801 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'C' and resid 2121 through 2127 Processing sheet with id= AQ, first strand: chain 'C' and resid 2396 through 2398 Processing sheet with id= AR, first strand: chain 'C' and resid 13 through 18 removed outlier: 6.264A pdb=" N SER C 15 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU C 223 " --> pdb=" O SER C 15 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TYR C 17 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE C 221 " --> pdb=" O TYR C 17 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 132 through 140 removed outlier: 3.733A pdb=" N ARG C 149 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= AU, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.786A pdb=" N SER D 120 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'D' and resid 194 through 196 Processing sheet with id= AW, first strand: chain 'D' and resid 242 through 245 Processing sheet with id= AX, first strand: chain 'D' and resid 252 through 257 Processing sheet with id= AY, first strand: chain 'D' and resid 283 through 287 Processing sheet with id= AZ, first strand: chain 'D' and resid 314 through 319 Processing sheet with id= BA, first strand: chain 'D' and resid 369 through 371 Processing sheet with id= BB, first strand: chain 'D' and resid 397 through 400 Processing sheet with id= BC, first strand: chain 'D' and resid 667 through 670 Processing sheet with id= BD, first strand: chain 'D' and resid 800 through 802 removed outlier: 6.298A pdb=" N GLN D1096 " --> pdb=" O ARG D 801 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'D' and resid 2121 through 2127 Processing sheet with id= BF, first strand: chain 'D' and resid 2396 through 2398 Processing sheet with id= BG, first strand: chain 'D' and resid 13 through 18 removed outlier: 6.264A pdb=" N SER D 15 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU D 223 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TYR D 17 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE D 221 " --> pdb=" O TYR D 17 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'D' and resid 132 through 140 removed outlier: 3.733A pdb=" N ARG D 149 " --> pdb=" O ASN D 136 " (cutoff:3.500A) 3480 hydrogen bonds defined for protein. 9636 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: 31.36 Time building geometry restraints manager: 25.79 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: 22412 1.34 - 1.46: 14980 1.46 - 1.58: 31680 1.58 - 1.70: 28 1.70 - 1.81: 652 Bond restraints: 69752 Sorted by residual: bond pdb=" O4 I3P B2702 " pdb=" P4 I3P B2702 " ideal model delta sigma weight residual 1.697 1.644 0.053 2.00e-02 2.50e+03 7.04e+00 bond pdb=" O4 I3P A2702 " pdb=" P4 I3P A2702 " ideal model delta sigma weight residual 1.697 1.644 0.053 2.00e-02 2.50e+03 6.95e+00 bond pdb=" O4 I3P D2702 " pdb=" P4 I3P D2702 " ideal model delta sigma weight residual 1.697 1.644 0.053 2.00e-02 2.50e+03 6.95e+00 bond pdb=" O5 I3P A2702 " pdb=" P5 I3P A2702 " ideal model delta sigma weight residual 1.695 1.643 0.052 2.00e-02 2.50e+03 6.87e+00 bond pdb=" O5 I3P B2702 " pdb=" P5 I3P B2702 " ideal model delta sigma weight residual 1.695 1.643 0.052 2.00e-02 2.50e+03 6.87e+00 ... (remaining 69747 not shown) Histogram of bond angle deviations from ideal: 99.05 - 107.21: 1935 107.21 - 115.37: 43145 115.37 - 123.53: 47723 123.53 - 131.69: 1373 131.69 - 139.85: 88 Bond angle restraints: 94264 Sorted by residual: angle pdb=" N ILE B2278 " pdb=" CA ILE B2278 " pdb=" C ILE B2278 " ideal model delta sigma weight residual 110.30 106.48 3.82 9.70e-01 1.06e+00 1.55e+01 angle pdb=" N ILE A2278 " pdb=" CA ILE A2278 " pdb=" C ILE A2278 " ideal model delta sigma weight residual 110.30 106.48 3.82 9.70e-01 1.06e+00 1.55e+01 angle pdb=" N ILE C2278 " pdb=" CA ILE C2278 " pdb=" C ILE C2278 " ideal model delta sigma weight residual 110.30 106.48 3.82 9.70e-01 1.06e+00 1.55e+01 angle pdb=" N ILE D2278 " pdb=" CA ILE D2278 " pdb=" C ILE D2278 " ideal model delta sigma weight residual 110.30 106.51 3.79 9.70e-01 1.06e+00 1.53e+01 angle pdb=" CA GLY C2475 " pdb=" C GLY C2475 " pdb=" O GLY C2475 " ideal model delta sigma weight residual 122.59 117.87 4.72 1.27e+00 6.20e-01 1.38e+01 ... (remaining 94259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 38040 17.54 - 35.08: 3459 35.08 - 52.61: 533 52.61 - 70.15: 64 70.15 - 87.69: 48 Dihedral angle restraints: 42144 sinusoidal: 17232 harmonic: 24912 Sorted by residual: dihedral pdb=" CA LYS C1379 " pdb=" C LYS C1379 " pdb=" N ASN C1380 " pdb=" CA ASN C1380 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LYS D1379 " pdb=" C LYS D1379 " pdb=" N ASN D1380 " pdb=" CA ASN D1380 " ideal model delta harmonic sigma weight residual 180.00 159.07 20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LYS B1379 " pdb=" C LYS B1379 " pdb=" N ASN B1380 " pdb=" CA ASN B1380 " ideal model delta harmonic sigma weight residual 180.00 159.07 20.93 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 42141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 9644 0.058 - 0.117: 1112 0.117 - 0.175: 72 0.175 - 0.234: 0 0.234 - 0.292: 12 Chirality restraints: 10840 Sorted by residual: chirality pdb=" C2' ATP A2703 " pdb=" C1' ATP A2703 " pdb=" C3' ATP A2703 " pdb=" O2' ATP A2703 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP B2703 " pdb=" C1' ATP B2703 " pdb=" C3' ATP B2703 " pdb=" O2' ATP B2703 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP C2703 " pdb=" C1' ATP C2703 " pdb=" C3' ATP C2703 " pdb=" O2' ATP C2703 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 10837 not shown) Planarity restraints: 11928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A2470 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C LEU A2470 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A2470 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG A2471 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B2470 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C LEU B2470 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU B2470 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG B2471 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D2470 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C LEU D2470 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU D2470 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG D2471 " 0.012 2.00e-02 2.50e+03 ... (remaining 11925 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 1028 2.64 - 3.20: 68585 3.20 - 3.77: 108347 3.77 - 4.33: 147015 4.33 - 4.90: 242095 Nonbonded interactions: 567070 Sorted by model distance: nonbonded pdb=" O VAL C2553 " pdb=" OG SER C2554 " model vdw 2.071 2.440 nonbonded pdb=" O VAL A2553 " pdb=" OG SER A2554 " model vdw 2.071 2.440 nonbonded pdb=" O VAL B2553 " pdb=" OG SER B2554 " model vdw 2.071 2.440 nonbonded pdb=" O VAL D2553 " pdb=" OG SER D2554 " model vdw 2.071 2.440 nonbonded pdb=" OG1 THR C1255 " pdb=" OE1 GLU C1260 " model vdw 2.094 2.440 ... (remaining 567065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 24 5.49 5 S 412 5.16 5 C 43696 2.51 5 N 11712 2.21 5 O 12664 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 8.870 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: 0.060 Extract box with map and model: 26.280 Check model and map are aligned: 0.790 Convert atoms to be neutral: 0.470 Process input model: 153.660 Find NCS groups from input model: 4.340 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 69752 Z= 0.198 Angle : 0.532 8.499 94264 Z= 0.293 Chirality : 0.037 0.292 10840 Planarity : 0.003 0.060 11928 Dihedral : 13.420 87.690 25876 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.10), residues: 8232 helix: 2.03 (0.07), residues: 5104 sheet: -1.43 (0.19), residues: 660 loop : -0.74 (0.13), residues: 2468 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2332 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2328 time to evaluate : 6.539 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 2332 average time/residue: 0.6481 time to fit residues: 2548.7599 Evaluate side-chains 1155 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1155 time to evaluate : 6.454 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.7539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 716 optimal weight: 10.0000 chunk 642 optimal weight: 2.9990 chunk 356 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 433 optimal weight: 10.0000 chunk 343 optimal weight: 8.9990 chunk 664 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 404 optimal weight: 7.9990 chunk 494 optimal weight: 0.0970 chunk 770 optimal weight: 10.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 625 ASN A 843 ASN A1065 HIS A1081 HIS A1199 ASN ** A1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1266 HIS ** A1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 ASN A1746 ASN A1902 ASN A1953 HIS ** A1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2153 HIS A2292 ASN A2467 ASN ** A2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN B 843 ASN B1065 HIS B1081 HIS B1199 ASN ** B1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1266 HIS ** B1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1477 ASN B1746 ASN B1902 ASN B1909 GLN B1953 HIS ** B1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2153 HIS B2292 ASN B2467 ASN ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 ASN C 625 ASN C 843 ASN C1065 HIS C1081 HIS C1193 GLN C1199 ASN ** C1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1266 HIS C1402 HIS ** C1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1477 ASN C1746 ASN C1902 ASN C1953 HIS ** C1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2153 HIS C2292 ASN C2467 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 ASN ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN D 625 ASN D 843 ASN D1065 HIS D1081 HIS D1199 ASN ** D1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1266 HIS D1402 HIS D1477 ASN D1746 ASN D1902 ASN D1953 HIS ** D1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2153 HIS D2292 ASN D2467 ASN ** D2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 69752 Z= 0.404 Angle : 0.723 11.869 94264 Z= 0.372 Chirality : 0.044 0.211 10840 Planarity : 0.006 0.073 11928 Dihedral : 4.697 44.263 9084 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.09), residues: 8232 helix: 1.41 (0.07), residues: 5112 sheet: -1.22 (0.20), residues: 600 loop : -0.84 (0.13), residues: 2520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1157 time to evaluate : 6.509 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: 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: 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: 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 outliers start: 261 outliers final: 193 residues processed: 1323 average time/residue: 0.6336 time to fit residues: 1469.7427 Evaluate side-chains 1067 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 874 time to evaluate : 6.515 Switching outliers to nearest non-outliers outliers start: 193 outliers final: 0 residues processed: 193 average time/residue: 0.4875 time to fit residues: 188.6317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 427 optimal weight: 0.8980 chunk 238 optimal weight: 0.9980 chunk 640 optimal weight: 4.9990 chunk 524 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 771 optimal weight: 8.9990 chunk 833 optimal weight: 3.9990 chunk 687 optimal weight: 0.7980 chunk 765 optimal weight: 7.9990 chunk 263 optimal weight: 0.6980 chunk 618 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 703 HIS A1094 GLN A1193 GLN A1199 ASN ** A1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1402 HIS ** A1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 ASN A1953 HIS ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2510 ASN A2550 ASN B 70 GLN B 703 HIS B1193 GLN ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1402 HIS ** B1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1477 ASN B1797 GLN B1953 HIS ** B1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2550 ASN C 70 GLN C 703 HIS C1094 GLN C1199 ASN ** C1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1477 ASN C1953 HIS ** C2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2550 ASN D 70 GLN D 703 HIS D1094 GLN D1193 GLN D1199 ASN ** D1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1477 ASN D1953 HIS ** D2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2550 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 69752 Z= 0.196 Angle : 0.604 12.569 94264 Z= 0.305 Chirality : 0.040 0.273 10840 Planarity : 0.004 0.058 11928 Dihedral : 4.436 43.098 9084 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.09), residues: 8232 helix: 1.48 (0.07), residues: 5080 sheet: -1.10 (0.20), residues: 596 loop : -0.72 (0.13), residues: 2556 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1065 time to evaluate : 6.535 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 56 residues processed: 1142 average time/residue: 0.5979 time to fit residues: 1197.4861 Evaluate side-chains 966 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 910 time to evaluate : 6.531 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.4865 time to fit residues: 60.5036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 762 optimal weight: 0.4980 chunk 580 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 368 optimal weight: 10.0000 chunk 518 optimal weight: 5.9990 chunk 774 optimal weight: 10.0000 chunk 819 optimal weight: 1.9990 chunk 404 optimal weight: 7.9990 chunk 733 optimal weight: 0.0060 chunk 220 optimal weight: 10.0000 overall best weight: 3.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 HIS ** A1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1693 ASN ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2510 ASN B 103 GLN B 384 ASN ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN B1065 HIS ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1693 ASN B1773 HIS B1797 GLN ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2210 ASN B2510 ASN C 103 GLN C 384 ASN ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** C1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1265 GLN C1402 HIS ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2210 ASN C2510 ASN D 103 GLN D 384 ASN ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1065 HIS ** D1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1265 GLN ** D1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2210 ASN D2510 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 69752 Z= 0.303 Angle : 0.638 13.137 94264 Z= 0.322 Chirality : 0.041 0.216 10840 Planarity : 0.004 0.054 11928 Dihedral : 4.466 39.535 9084 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.09), residues: 8232 helix: 1.37 (0.07), residues: 5068 sheet: -0.69 (0.22), residues: 536 loop : -0.86 (0.12), residues: 2628 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 972 time to evaluate : 6.588 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: 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: 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: symmetry clash outliers start: 183 outliers final: 106 residues processed: 1078 average time/residue: 0.6508 time to fit residues: 1243.6638 Evaluate side-chains 956 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 850 time to evaluate : 6.527 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 0 residues processed: 106 average time/residue: 0.4864 time to fit residues: 110.4558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 682 optimal weight: 3.9990 chunk 465 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 610 optimal weight: 9.9990 chunk 338 optimal weight: 0.0870 chunk 699 optimal weight: 20.0000 chunk 566 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 418 optimal weight: 0.9990 chunk 735 optimal weight: 8.9990 chunk 206 optimal weight: 0.9980 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN A 502 ASN A1061 HIS ** A1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS ** A1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN B1061 HIS ** B1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1650 HIS B1693 ASN B1797 GLN B1909 GLN ** B1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 502 ASN C1061 HIS C1265 GLN ** C1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1650 HIS ** C1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN D 502 ASN D1061 HIS ** D1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1265 GLN ** D1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1494 HIS D1650 HIS ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 69752 Z= 0.185 Angle : 0.597 10.667 94264 Z= 0.298 Chirality : 0.039 0.198 10840 Planarity : 0.004 0.044 11928 Dihedral : 4.354 38.025 9084 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 8232 helix: 1.32 (0.07), residues: 5072 sheet: -0.67 (0.22), residues: 564 loop : -0.78 (0.12), residues: 2596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 994 time to evaluate : 7.034 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 49 residues processed: 1060 average time/residue: 0.6062 time to fit residues: 1123.8956 Evaluate side-chains 922 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 873 time to evaluate : 6.558 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.4961 time to fit residues: 55.3183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 275 optimal weight: 20.0000 chunk 738 optimal weight: 0.0060 chunk 162 optimal weight: 8.9990 chunk 481 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 820 optimal weight: 6.9990 chunk 681 optimal weight: 5.9990 chunk 379 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 271 optimal weight: 6.9990 chunk 430 optimal weight: 10.0000 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 384 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 HIS ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 GLN A1266 HIS ** A1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2210 ASN ** A2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 384 ASN ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1065 HIS ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1265 GLN B1266 HIS ** B1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1650 HIS ** B1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2510 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN C 384 ASN ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** C1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1265 GLN C1266 HIS ** C1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2510 ASN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN D 384 ASN ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1065 HIS ** D1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1265 GLN D1266 HIS ** D1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2510 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 69752 Z= 0.372 Angle : 0.666 12.678 94264 Z= 0.338 Chirality : 0.042 0.314 10840 Planarity : 0.004 0.046 11928 Dihedral : 4.512 34.271 9084 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 8232 helix: 1.20 (0.07), residues: 5056 sheet: -0.43 (0.23), residues: 536 loop : -0.92 (0.12), residues: 2640 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 895 time to evaluate : 6.544 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 159 outliers final: 103 residues processed: 991 average time/residue: 0.6156 time to fit residues: 1069.9397 Evaluate side-chains 935 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 832 time to evaluate : 6.485 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 0 residues processed: 103 average time/residue: 0.4974 time to fit residues: 106.9424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 791 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 467 optimal weight: 0.8980 chunk 599 optimal weight: 6.9990 chunk 464 optimal weight: 0.7980 chunk 690 optimal weight: 6.9990 chunk 458 optimal weight: 1.9990 chunk 817 optimal weight: 8.9990 chunk 511 optimal weight: 7.9990 chunk 498 optimal weight: 30.0000 chunk 377 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 HIS A1285 HIS ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2510 ASN ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 HIS B1285 HIS ** B1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1650 HIS ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 HIS ** C1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1285 HIS ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1650 HIS C1670 GLN ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1061 HIS D1285 HIS ** D1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1650 HIS ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 69752 Z= 0.207 Angle : 0.619 12.186 94264 Z= 0.310 Chirality : 0.040 0.291 10840 Planarity : 0.004 0.043 11928 Dihedral : 4.392 31.860 9084 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.09), residues: 8232 helix: 1.22 (0.07), residues: 5036 sheet: -0.41 (0.23), residues: 536 loop : -0.87 (0.12), residues: 2660 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 951 time to evaluate : 6.506 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: 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: 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: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 26 residues processed: 1013 average time/residue: 0.6097 time to fit residues: 1082.8468 Evaluate side-chains 884 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 858 time to evaluate : 6.512 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.5401 time to fit residues: 34.4520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 505 optimal weight: 0.9990 chunk 326 optimal weight: 7.9990 chunk 488 optimal weight: 30.0000 chunk 246 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 519 optimal weight: 10.0000 chunk 556 optimal weight: 5.9990 chunk 404 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 642 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 ASN A 564 GLN A 661 ASN A1065 HIS ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 HIS ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2510 ASN B 384 ASN ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 661 ASN B1065 HIS ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2510 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 661 ASN C 783 HIS C1065 HIS ** C1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1296 HIS ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1670 GLN ** C2063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 ASN ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 GLN D 661 ASN D 783 HIS D1065 HIS ** D1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1199 ASN ** D1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1296 HIS ** D1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 69752 Z= 0.248 Angle : 0.652 13.577 94264 Z= 0.324 Chirality : 0.041 0.316 10840 Planarity : 0.004 0.043 11928 Dihedral : 4.412 31.360 9084 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.09), residues: 8232 helix: 1.12 (0.07), residues: 5044 sheet: -0.61 (0.22), residues: 568 loop : -0.88 (0.12), residues: 2620 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 925 time to evaluate : 6.601 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 46 residues processed: 982 average time/residue: 0.6240 time to fit residues: 1076.1269 Evaluate side-chains 894 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 848 time to evaluate : 6.531 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.5315 time to fit residues: 54.1987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 743 optimal weight: 6.9990 chunk 783 optimal weight: 7.9990 chunk 714 optimal weight: 9.9990 chunk 761 optimal weight: 9.9990 chunk 782 optimal weight: 10.0000 chunk 458 optimal weight: 0.9980 chunk 331 optimal weight: 1.9990 chunk 598 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 688 optimal weight: 3.9990 chunk 720 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1061 HIS ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 ASN ** A1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2510 ASN ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B1061 HIS ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1296 HIS ** B1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1650 HIS ** B1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C1061 HIS C1199 ASN ** C1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1650 HIS C2063 HIS ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2510 ASN D 76 GLN ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 GLN D1061 HIS ** D1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1650 HIS ** D1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2510 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 69752 Z= 0.345 Angle : 0.711 12.618 94264 Z= 0.354 Chirality : 0.043 0.351 10840 Planarity : 0.004 0.064 11928 Dihedral : 4.584 31.956 9084 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.09), residues: 8232 helix: 0.97 (0.07), residues: 5056 sheet: -0.71 (0.23), residues: 536 loop : -0.97 (0.12), residues: 2640 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 880 time to evaluate : 6.895 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 36 residues processed: 913 average time/residue: 0.6165 time to fit residues: 988.6732 Evaluate side-chains 866 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 830 time to evaluate : 6.523 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.5232 time to fit residues: 43.7704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 758 optimal weight: 0.8980 chunk 500 optimal weight: 8.9990 chunk 805 optimal weight: 9.9990 chunk 491 optimal weight: 10.0000 chunk 382 optimal weight: 10.0000 chunk 559 optimal weight: 0.0050 chunk 844 optimal weight: 10.0000 chunk 777 optimal weight: 0.4980 chunk 672 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 519 optimal weight: 7.9990 overall best weight: 2.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 384 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN A1065 HIS ** A1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1065 HIS ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1650 HIS ** B2063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** C1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1650 HIS ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 ASN ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 843 ASN D1065 HIS ** D1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1650 HIS ** D2008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.105 69752 Z= 0.245 Angle : 0.703 16.690 94264 Z= 0.344 Chirality : 0.041 0.396 10840 Planarity : 0.004 0.065 11928 Dihedral : 4.538 32.133 9084 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.09), residues: 8232 helix: 0.97 (0.07), residues: 5036 sheet: -0.61 (0.23), residues: 528 loop : -0.89 (0.12), residues: 2668 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16464 Ramachandran restraints generated. 8232 Oldfield, 0 Emsley, 8232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 908 time to evaluate : 6.586 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 23 residues processed: 923 average time/residue: 0.6611 time to fit residues: 1078.2983 Evaluate side-chains 869 residues out of total 7636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 846 time to evaluate : 6.547 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4998 time to fit residues: 30.9388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 412 optimal weight: 0.2980 chunk 534 optimal weight: 9.9990 chunk 716 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 620 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 673 optimal weight: 0.7980 chunk 281 optimal weight: 3.9990 chunk 691 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 HIS A1094 GLN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS ** A1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 HIS ** C1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1650 HIS ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1061 HIS ** D1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1650 HIS ** D2008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2174 GLN ** D2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.116122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.087404 restraints weight = 180997.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.087441 restraints weight = 101285.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.087921 restraints weight = 70569.102| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 69752 Z= 0.212 Angle : 0.692 13.415 94264 Z= 0.341 Chirality : 0.041 0.382 10840 Planarity : 0.004 0.068 11928 Dihedral : 4.487 32.210 9084 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.09), residues: 8232 helix: 0.99 (0.07), residues: 5024 sheet: -0.58 (0.23), residues: 528 loop : -0.91 (0.12), residues: 2680 =============================================================================== Job complete usr+sys time: 18110.86 seconds wall clock time: 318 minutes 8.26 seconds (19088.26 seconds total)