Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 08:37:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3r_25669/04_2023/7t3r_25669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3r_25669/04_2023/7t3r_25669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3r_25669/04_2023/7t3r_25669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3r_25669/04_2023/7t3r_25669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3r_25669/04_2023/7t3r_25669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3r_25669/04_2023/7t3r_25669_updated.pdb" } resolution = 3.4 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= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 S 416 5.16 5 C 43864 2.51 5 N 11756 2.21 5 O 12716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2388": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 68780 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 17139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2130, 17139 Classifications: {'peptide': 2130} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 58, 'TRANS': 2071} Chain breaks: 21 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 2, 'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 17139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2130, 17139 Classifications: {'peptide': 2130} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 58, 'TRANS': 2071} Chain breaks: 21 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 2, 'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 17139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2130, 17139 Classifications: {'peptide': 2130} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 58, 'TRANS': 2071} Chain breaks: 21 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 2, 'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 17139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2130, 17139 Classifications: {'peptide': 2130} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 58, 'TRANS': 2071} Chain breaks: 21 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 2, 'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16421 SG CYS A2538 99.616 129.057 102.353 1.00 47.87 S ATOM 16446 SG CYS A2541 100.731 126.753 99.455 1.00 49.31 S ATOM 33560 SG CYS B2538 109.453 99.589 102.374 1.00 45.40 S ATOM 33585 SG CYS B2541 111.712 100.746 99.455 1.00 47.41 S ATOM 50699 SG CYS C2538 138.906 109.543 102.387 1.00 48.18 S ATOM 50724 SG CYS C2541 137.742 111.740 99.433 1.00 49.94 S ATOM 67838 SG CYS D2538 129.060 138.849 102.382 1.00 50.80 S ATOM 67863 SG CYS D2541 126.757 137.741 99.468 1.00 52.25 S Time building chain proxies: 25.89, per 1000 atoms: 0.38 Number of scatterers: 68780 At special positions: 0 Unit cell: (239.292, 239.292, 182.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 416 16.00 P 24 15.00 O 12716 8.00 N 11756 7.00 C 43864 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: 23.23 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2701 " pdb="ZN ZN A2701 " - pdb=" NE2 HIS A2558 " pdb="ZN ZN A2701 " - pdb=" ND1 HIS A2563 " pdb="ZN ZN A2701 " - pdb=" SG CYS A2541 " pdb="ZN ZN A2701 " - pdb=" SG CYS A2538 " pdb=" ZN B2701 " pdb="ZN ZN B2701 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B2701 " - pdb=" ND1 HIS B2563 " pdb="ZN ZN B2701 " - pdb=" SG CYS B2541 " pdb="ZN ZN B2701 " - pdb=" SG CYS B2538 " pdb=" ZN C2701 " pdb="ZN ZN C2701 " - pdb=" NE2 HIS C2558 " pdb="ZN ZN C2701 " - pdb=" ND1 HIS C2563 " pdb="ZN ZN C2701 " - pdb=" SG CYS C2541 " pdb="ZN ZN C2701 " - pdb=" SG CYS C2538 " pdb=" ZN D2701 " pdb="ZN ZN D2701 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D2701 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D2701 " - pdb=" SG CYS D2541 " pdb="ZN ZN D2701 " - pdb=" SG CYS D2538 " Number of angles added : 4 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 400 helices and 60 sheets defined 60.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.99 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 511 Processing helix chain 'A' and resid 514 through 524 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: 4.218A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLY A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 599 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 638 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 Processing helix chain 'A' and resid 745 through 754 removed outlier: 4.409A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (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 854 through 873 removed outlier: 4.167A pdb=" N LYS A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 892 Processing helix chain 'A' and resid 962 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 1081 Processing helix chain 'A' and resid 1084 through 1094 Processing helix chain 'A' and resid 1101 through 1122 Processing helix chain 'A' and resid 1124 through 1126 No H-bonds generated for 'chain 'A' and resid 1124 through 1126' Processing helix chain 'A' and resid 1169 through 1183 Processing helix chain 'A' and resid 1187 through 1199 removed outlier: 3.704A pdb=" N LYS A1191 " --> pdb=" O GLU A1187 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A1192 " --> pdb=" O GLN A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1211 Processing helix chain 'A' and resid 1219 through 1235 Processing helix chain 'A' and resid 1240 through 1249 removed outlier: 3.837A pdb=" N LYS A1248 " --> pdb=" O ALA A1244 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N HIS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 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 1307 Processing helix chain 'A' and resid 1315 through 1331 removed outlier: 3.708A pdb=" N MET A1322 " --> pdb=" O GLN A1318 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP A1330 " --> pdb=" O THR A1326 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASP A1331 " --> pdb=" O ASN A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1351 Processing helix chain 'A' and resid 1361 through 1376 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 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1436 through 1450 Processing helix chain 'A' and resid 1463 through 1481 removed outlier: 3.793A pdb=" N VAL A1472 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1507 Processing helix chain 'A' and resid 1521 through 1533 removed outlier: 3.613A pdb=" N MET A1531 " --> pdb=" O ARG A1527 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A1532 " --> pdb=" O THR A1528 " (cutoff:3.500A) removed outlier: 3.663A 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: 4.365A pdb=" N GLN A1611 " --> pdb=" O LYS A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1639 Processing helix chain 'A' and resid 1642 through 1657 removed outlier: 4.242A pdb=" N LEU A1647 " --> pdb=" O PHE A1643 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A1655 " --> pdb=" O THR A1651 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU A1656 " --> pdb=" O LYS A1652 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER A1657 " --> pdb=" O ASP A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1673 Processing helix chain 'A' and resid 1682 through 1694 Processing helix chain 'A' and resid 1719 through 1731 Processing helix chain 'A' and resid 1733 through 1743 Processing helix chain 'A' and resid 1747 through 1761 Processing helix chain 'A' and resid 1766 through 1778 Processing helix chain 'A' and resid 1780 through 1802 removed outlier: 3.503A pdb=" N PHE A1786 " --> pdb=" O GLU A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1865 through 1880 removed outlier: 4.083A pdb=" N MET A1870 " --> pdb=" O SER A1866 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN A1871 " --> pdb=" O VAL A1867 " (cutoff:3.500A) Proline residue: A1872 - end of helix Processing helix chain 'A' and resid 1886 through 1891 Processing helix chain 'A' and resid 1903 through 1915 removed outlier: 3.519A pdb=" N LEU A1908 " --> pdb=" O VAL A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1921 Processing helix chain 'A' and resid 1925 through 1928 No H-bonds generated for 'chain 'A' and resid 1925 through 1928' Processing helix chain 'A' and resid 1934 through 1948 Processing helix chain 'A' and resid 1953 through 1960 Processing helix chain 'A' and resid 1966 through 1975 Processing helix chain 'A' and resid 1979 through 1984 removed outlier: 4.489A pdb=" N TYR A1984 " --> pdb=" O PRO A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 2004 removed outlier: 3.702A pdb=" N MET A2004 " --> pdb=" O LEU A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2011 through 2019 Processing helix chain 'A' and resid 2022 through 2034 Processing helix chain 'A' and resid 2046 through 2063 removed outlier: 3.902A pdb=" N ARG A2062 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 4.955A 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: 4.266A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A2190 " --> pdb=" O ARG A2186 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2221 removed outlier: 3.871A pdb=" N ARG A2200 " --> pdb=" O TRP A2196 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N THR A2202 " --> pdb=" O SER A2198 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A2203 " --> pdb=" O ARG A2199 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A2204 " --> pdb=" O ARG A2200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A2205 " --> pdb=" O MET A2201 " (cutoff:3.500A) Processing helix chain 'A' and resid 2262 through 2304 removed outlier: 7.389A pdb=" N ILE A2278 " --> pdb=" O TYR A2274 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N GLY A2279 " --> pdb=" O TYR A2275 " (cutoff:3.500A) Proline residue: A2280 - end of helix Processing helix chain 'A' and resid 2319 through 2335 Processing helix chain 'A' and resid 2340 through 2345 Processing helix chain 'A' and resid 2348 through 2351 No H-bonds generated for 'chain 'A' and resid 2348 through 2351' Processing helix chain 'A' and resid 2353 through 2363 removed outlier: 3.770A pdb=" N VAL A2362 " --> pdb=" O VAL A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2366 through 2390 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 2536 removed outlier: 4.198A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A2515 " --> pdb=" O LEU A2511 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A2516 " --> pdb=" O ILE A2512 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2548 Processing helix chain 'A' and resid 2565 through 2577 removed outlier: 3.559A pdb=" N LEU A2569 " --> pdb=" O MET A2565 " (cutoff:3.500A) 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 2596 Processing helix chain 'A' and resid 2608 through 2610 No H-bonds generated for 'chain 'A' and resid 2608 through 2610' Processing helix chain 'A' and resid 2629 through 2645 removed outlier: 3.913A pdb=" N UNK A2645 " --> pdb=" O UNK A2641 " (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 511 Processing helix chain 'B' and resid 514 through 524 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: 4.250A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLY B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N MET B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 599 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 638 Processing helix chain 'B' and resid 646 through 656 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 Processing helix chain 'B' and resid 745 through 754 removed outlier: 4.421A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (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 854 through 873 removed outlier: 4.132A pdb=" N LYS B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 859 " --> pdb=" O GLU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 892 Processing helix chain 'B' and resid 962 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 1081 Processing helix chain 'B' and resid 1084 through 1094 Processing helix chain 'B' and resid 1101 through 1122 Processing helix chain 'B' and resid 1124 through 1126 No H-bonds generated for 'chain 'B' and resid 1124 through 1126' Processing helix chain 'B' and resid 1169 through 1183 Processing helix chain 'B' and resid 1187 through 1199 removed outlier: 3.773A pdb=" N LYS B1191 " --> pdb=" O GLU B1187 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B1192 " --> pdb=" O GLN B1188 " (cutoff:3.500A) Processing helix chain 'B' and resid 1203 through 1211 Processing helix chain 'B' and resid 1219 through 1235 Processing helix chain 'B' and resid 1240 through 1249 removed outlier: 3.872A pdb=" N LYS B1248 " --> pdb=" O ALA B1244 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) Processing helix chain 'B' and resid 1258 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 1307 Processing helix chain 'B' and resid 1315 through 1331 removed outlier: 3.708A pdb=" N MET B1322 " --> pdb=" O GLN B1318 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B1330 " --> pdb=" O THR B1326 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ASP B1331 " --> pdb=" O ASN B1327 " (cutoff:3.500A) Processing helix chain 'B' and resid 1339 through 1351 Processing helix chain 'B' and resid 1361 through 1376 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 1432 No H-bonds generated for 'chain 'B' and resid 1430 through 1432' Processing helix chain 'B' and resid 1436 through 1450 removed outlier: 3.510A pdb=" N LEU B1446 " --> pdb=" O GLU B1442 " (cutoff:3.500A) Processing helix chain 'B' and resid 1463 through 1481 removed outlier: 3.787A pdb=" N VAL B1472 " --> pdb=" O VAL B1468 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU B1473 " --> pdb=" O LEU B1469 " (cutoff:3.500A) Processing helix chain 'B' and resid 1494 through 1507 Processing helix chain 'B' and resid 1521 through 1533 removed outlier: 3.619A pdb=" N MET B1531 " --> pdb=" O ARG B1527 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B1532 " --> pdb=" O THR B1528 " (cutoff:3.500A) removed outlier: 3.665A 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: 4.370A pdb=" N GLN B1611 " --> pdb=" O LYS B1607 " (cutoff:3.500A) Processing helix chain 'B' and resid 1633 through 1640 Processing helix chain 'B' and resid 1642 through 1657 removed outlier: 4.514A pdb=" N LEU B1647 " --> pdb=" O PHE B1643 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET B1655 " --> pdb=" O THR B1651 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU B1656 " --> pdb=" O LYS B1652 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER B1657 " --> pdb=" O ASP B1653 " (cutoff:3.500A) Processing helix chain 'B' and resid 1659 through 1673 Processing helix chain 'B' and resid 1682 through 1694 Processing helix chain 'B' and resid 1719 through 1731 Processing helix chain 'B' and resid 1733 through 1743 Processing helix chain 'B' and resid 1747 through 1761 Processing helix chain 'B' and resid 1766 through 1778 Processing helix chain 'B' and resid 1780 through 1802 removed outlier: 3.506A pdb=" N PHE B1786 " --> pdb=" O GLU B1783 " (cutoff:3.500A) Processing helix chain 'B' and resid 1865 through 1880 removed outlier: 4.159A pdb=" N MET B1870 " --> pdb=" O SER B1866 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN B1871 " --> pdb=" O VAL B1867 " (cutoff:3.500A) Proline residue: B1872 - end of helix Processing helix chain 'B' and resid 1886 through 1891 Processing helix chain 'B' and resid 1903 through 1915 Processing helix chain 'B' and resid 1918 through 1921 No H-bonds generated for 'chain 'B' and resid 1918 through 1921' Processing helix chain 'B' and resid 1925 through 1928 No H-bonds generated for 'chain 'B' and resid 1925 through 1928' Processing helix chain 'B' and resid 1934 through 1948 Processing helix chain 'B' and resid 1953 through 1960 Processing helix chain 'B' and resid 1966 through 1975 Processing helix chain 'B' and resid 1979 through 1984 removed outlier: 4.399A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1987 through 2004 removed outlier: 3.707A pdb=" N MET B2004 " --> pdb=" O LEU B2000 " (cutoff:3.500A) Processing helix chain 'B' and resid 2011 through 2019 Processing helix chain 'B' and resid 2022 through 2034 Processing helix chain 'B' and resid 2046 through 2063 removed outlier: 3.887A pdb=" N ARG B2062 " --> pdb=" O LEU B2058 " (cutoff:3.500A) removed outlier: 4.962A 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: 4.272A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B2190 " --> pdb=" O ARG B2186 " (cutoff:3.500A) Processing helix chain 'B' and resid 2192 through 2199 Processing helix chain 'B' and resid 2201 through 2221 removed outlier: 3.508A pdb=" N GLY B2205 " --> pdb=" O MET B2201 " (cutoff:3.500A) Processing helix chain 'B' and resid 2262 through 2304 removed outlier: 7.345A pdb=" N ILE B2278 " --> pdb=" O TYR B2274 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N GLY B2279 " --> pdb=" O TYR B2275 " (cutoff:3.500A) Proline residue: B2280 - end of helix Processing helix chain 'B' and resid 2319 through 2335 Processing helix chain 'B' and resid 2340 through 2345 Processing helix chain 'B' and resid 2348 through 2351 No H-bonds generated for 'chain 'B' and resid 2348 through 2351' Processing helix chain 'B' and resid 2353 through 2363 removed outlier: 3.786A pdb=" N VAL B2362 " --> pdb=" O VAL B2358 " (cutoff:3.500A) Processing helix chain 'B' and resid 2366 through 2390 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 2536 removed outlier: 4.271A pdb=" N PHE B2513 " --> pdb=" O LEU B2509 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B2515 " --> pdb=" O LEU B2511 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B2516 " --> pdb=" O ILE B2512 " (cutoff:3.500A) Processing helix chain 'B' and resid 2545 through 2548 Processing helix chain 'B' and resid 2565 through 2577 removed outlier: 3.576A pdb=" N LEU B2569 " --> pdb=" O MET B2565 " (cutoff:3.500A) 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 2596 Processing helix chain 'B' and resid 2608 through 2610 No H-bonds generated for 'chain 'B' and resid 2608 through 2610' Processing helix chain 'B' and resid 2629 through 2645 removed outlier: 3.960A pdb=" N UNK B2645 " --> pdb=" O UNK B2641 " (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 511 Processing helix chain 'C' and resid 514 through 524 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: 4.252A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLY C 579 " --> pdb=" O ALA C 575 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET C 580 " --> pdb=" O LYS C 576 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 599 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 638 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 Processing helix chain 'C' and resid 745 through 754 removed outlier: 4.376A pdb=" N GLU C 750 " --> pdb=" O LEU C 746 " (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 854 through 873 removed outlier: 4.116A pdb=" N LYS C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU C 859 " --> pdb=" O GLU C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 892 Processing helix chain 'C' and resid 962 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 1094 removed outlier: 3.859A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN C1084 " --> pdb=" O LYS C1080 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG C1085 " --> pdb=" O HIS C1081 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN C1086 " --> pdb=" O PHE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1122 Processing helix chain 'C' and resid 1124 through 1126 No H-bonds generated for 'chain 'C' and resid 1124 through 1126' Processing helix chain 'C' and resid 1169 through 1183 Processing helix chain 'C' and resid 1187 through 1199 removed outlier: 3.723A pdb=" N LYS C1191 " --> pdb=" O GLU C1187 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS C1192 " --> pdb=" O GLN C1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 1203 through 1211 Processing helix chain 'C' and resid 1219 through 1235 Processing helix chain 'C' and resid 1240 through 1249 removed outlier: 3.834A pdb=" N LYS C1248 " --> pdb=" O ALA C1244 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N HIS C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) Processing helix chain 'C' and resid 1258 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 1307 Processing helix chain 'C' and resid 1315 through 1331 removed outlier: 3.710A pdb=" N MET C1322 " --> pdb=" O GLN C1318 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP C1330 " --> pdb=" O THR C1326 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP C1331 " --> pdb=" O ASN C1327 " (cutoff:3.500A) Processing helix chain 'C' and resid 1339 through 1351 Processing helix chain 'C' and resid 1361 through 1376 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 1432 No H-bonds generated for 'chain 'C' and resid 1430 through 1432' Processing helix chain 'C' and resid 1436 through 1450 removed outlier: 3.511A pdb=" N LEU C1446 " --> pdb=" O GLU C1442 " (cutoff:3.500A) Processing helix chain 'C' and resid 1463 through 1481 removed outlier: 3.804A pdb=" N VAL C1472 " --> pdb=" O VAL C1468 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU C1473 " --> pdb=" O LEU C1469 " (cutoff:3.500A) Processing helix chain 'C' and resid 1494 through 1507 Processing helix chain 'C' and resid 1521 through 1533 removed outlier: 3.631A pdb=" N MET C1531 " --> pdb=" O ARG C1527 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL C1532 " --> pdb=" O THR C1528 " (cutoff:3.500A) removed outlier: 3.677A 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: 4.374A pdb=" N GLN C1611 " --> pdb=" O LYS C1607 " (cutoff:3.500A) Processing helix chain 'C' and resid 1633 through 1639 Processing helix chain 'C' and resid 1642 through 1657 removed outlier: 4.348A pdb=" N LEU C1647 " --> pdb=" O PHE C1643 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET C1655 " --> pdb=" O THR C1651 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU C1656 " --> pdb=" O LYS C1652 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER C1657 " --> pdb=" O ASP C1653 " (cutoff:3.500A) Processing helix chain 'C' and resid 1659 through 1673 Processing helix chain 'C' and resid 1682 through 1694 Processing helix chain 'C' and resid 1719 through 1731 Processing helix chain 'C' and resid 1733 through 1743 Processing helix chain 'C' and resid 1747 through 1761 Processing helix chain 'C' and resid 1766 through 1778 Processing helix chain 'C' and resid 1780 through 1802 removed outlier: 3.507A pdb=" N PHE C1786 " --> pdb=" O GLU C1783 " (cutoff:3.500A) Processing helix chain 'C' and resid 1865 through 1880 removed outlier: 4.143A pdb=" N MET C1870 " --> pdb=" O SER C1866 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN C1871 " --> pdb=" O VAL C1867 " (cutoff:3.500A) Proline residue: C1872 - end of helix Processing helix chain 'C' and resid 1886 through 1891 Processing helix chain 'C' and resid 1903 through 1915 Processing helix chain 'C' and resid 1917 through 1921 Processing helix chain 'C' and resid 1925 through 1928 No H-bonds generated for 'chain 'C' and resid 1925 through 1928' Processing helix chain 'C' and resid 1934 through 1949 Processing helix chain 'C' and resid 1953 through 1960 Processing helix chain 'C' and resid 1966 through 1975 Processing helix chain 'C' and resid 1979 through 1984 removed outlier: 4.514A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1987 through 2004 removed outlier: 3.727A pdb=" N MET C2004 " --> pdb=" O LEU C2000 " (cutoff:3.500A) Processing helix chain 'C' and resid 2011 through 2019 Processing helix chain 'C' and resid 2022 through 2034 Processing helix chain 'C' and resid 2046 through 2063 removed outlier: 3.915A pdb=" N ARG C2062 " --> pdb=" O LEU C2058 " (cutoff:3.500A) removed outlier: 4.974A 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: 4.287A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C2190 " --> pdb=" O ARG C2186 " (cutoff:3.500A) Processing helix chain 'C' and resid 2192 through 2221 removed outlier: 3.879A pdb=" N ARG C2200 " --> pdb=" O TRP C2196 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N THR C2202 " --> pdb=" O SER C2198 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C2203 " --> pdb=" O ARG C2199 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP C2204 " --> pdb=" O ARG C2200 " (cutoff:3.500A) Processing helix chain 'C' and resid 2262 through 2304 removed outlier: 7.342A pdb=" N ILE C2278 " --> pdb=" O TYR C2274 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLY C2279 " --> pdb=" O TYR C2275 " (cutoff:3.500A) Proline residue: C2280 - end of helix Processing helix chain 'C' and resid 2319 through 2335 Processing helix chain 'C' and resid 2340 through 2345 Processing helix chain 'C' and resid 2348 through 2351 No H-bonds generated for 'chain 'C' and resid 2348 through 2351' Processing helix chain 'C' and resid 2353 through 2363 removed outlier: 3.788A pdb=" N VAL C2362 " --> pdb=" O VAL C2358 " (cutoff:3.500A) Processing helix chain 'C' and resid 2366 through 2390 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 2536 removed outlier: 4.131A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C2515 " --> pdb=" O LEU C2511 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C2516 " --> pdb=" O ILE C2512 " (cutoff:3.500A) Processing helix chain 'C' and resid 2545 through 2548 Processing helix chain 'C' and resid 2565 through 2577 removed outlier: 3.549A pdb=" N LEU C2569 " --> pdb=" O MET C2565 " (cutoff:3.500A) 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 2596 Processing helix chain 'C' and resid 2608 through 2610 No H-bonds generated for 'chain 'C' and resid 2608 through 2610' Processing helix chain 'C' and resid 2629 through 2645 removed outlier: 4.017A pdb=" N UNK C2645 " --> pdb=" O UNK C2641 " (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 511 Processing helix chain 'D' and resid 514 through 524 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: 4.240A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 599 Processing helix chain 'D' and resid 603 through 609 Processing helix chain 'D' and resid 612 through 625 Processing helix chain 'D' and resid 628 through 638 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 Processing helix chain 'D' and resid 745 through 754 removed outlier: 4.332A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (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 854 through 873 removed outlier: 4.043A pdb=" N LYS D 858 " --> pdb=" O GLU D 854 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 892 Processing helix chain 'D' and resid 962 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 1081 Processing helix chain 'D' and resid 1084 through 1094 Processing helix chain 'D' and resid 1101 through 1122 Processing helix chain 'D' and resid 1124 through 1126 No H-bonds generated for 'chain 'D' and resid 1124 through 1126' Processing helix chain 'D' and resid 1169 through 1183 Processing helix chain 'D' and resid 1187 through 1199 removed outlier: 3.718A pdb=" N LYS D1191 " --> pdb=" O GLU D1187 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS D1192 " --> pdb=" O GLN D1188 " (cutoff:3.500A) Processing helix chain 'D' and resid 1203 through 1211 Processing helix chain 'D' and resid 1219 through 1235 Processing helix chain 'D' and resid 1240 through 1249 removed outlier: 3.841A pdb=" N LYS D1248 " --> pdb=" O ALA D1244 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) 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 1307 Processing helix chain 'D' and resid 1315 through 1331 removed outlier: 3.655A pdb=" N MET D1322 " --> pdb=" O GLN D1318 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP D1330 " --> pdb=" O THR D1326 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASP D1331 " --> pdb=" O ASN D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1339 through 1351 Processing helix chain 'D' and resid 1361 through 1376 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 1432 No H-bonds generated for 'chain 'D' and resid 1430 through 1432' Processing helix chain 'D' and resid 1436 through 1450 Processing helix chain 'D' and resid 1463 through 1481 removed outlier: 3.807A pdb=" N VAL D1472 " --> pdb=" O VAL D1468 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) Processing helix chain 'D' and resid 1494 through 1507 Processing helix chain 'D' and resid 1521 through 1533 removed outlier: 3.623A pdb=" N MET D1531 " --> pdb=" O ARG D1527 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL D1532 " --> pdb=" O THR D1528 " (cutoff:3.500A) removed outlier: 3.672A 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: 4.363A pdb=" N GLN D1611 " --> pdb=" O LYS D1607 " (cutoff:3.500A) Processing helix chain 'D' and resid 1633 through 1640 Processing helix chain 'D' and resid 1642 through 1657 removed outlier: 4.269A pdb=" N LEU D1647 " --> pdb=" O PHE D1643 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET D1655 " --> pdb=" O THR D1651 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLU D1656 " --> pdb=" O LYS D1652 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER D1657 " --> pdb=" O ASP D1653 " (cutoff:3.500A) Processing helix chain 'D' and resid 1659 through 1673 Processing helix chain 'D' and resid 1682 through 1694 Processing helix chain 'D' and resid 1719 through 1731 Processing helix chain 'D' and resid 1733 through 1743 Processing helix chain 'D' and resid 1747 through 1761 Processing helix chain 'D' and resid 1766 through 1778 Processing helix chain 'D' and resid 1780 through 1802 removed outlier: 3.505A pdb=" N PHE D1786 " --> pdb=" O GLU D1783 " (cutoff:3.500A) Processing helix chain 'D' and resid 1865 through 1880 removed outlier: 4.108A pdb=" N MET D1870 " --> pdb=" O SER D1866 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN D1871 " --> pdb=" O VAL D1867 " (cutoff:3.500A) Proline residue: D1872 - end of helix Processing helix chain 'D' and resid 1886 through 1891 Processing helix chain 'D' and resid 1903 through 1915 Processing helix chain 'D' and resid 1917 through 1921 Processing helix chain 'D' and resid 1925 through 1928 No H-bonds generated for 'chain 'D' and resid 1925 through 1928' Processing helix chain 'D' and resid 1934 through 1949 Processing helix chain 'D' and resid 1953 through 1960 Processing helix chain 'D' and resid 1966 through 1975 Processing helix chain 'D' and resid 1979 through 1984 removed outlier: 4.444A pdb=" N TYR D1984 " --> pdb=" O PRO D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1987 through 2004 removed outlier: 3.685A pdb=" N MET D2004 " --> pdb=" O LEU D2000 " (cutoff:3.500A) Processing helix chain 'D' and resid 2011 through 2019 Processing helix chain 'D' and resid 2022 through 2034 Processing helix chain 'D' and resid 2046 through 2063 removed outlier: 3.907A pdb=" N ARG D2062 " --> pdb=" O LEU D2058 " (cutoff:3.500A) removed outlier: 4.973A 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: 4.260A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER D2190 " --> pdb=" O ARG D2186 " (cutoff:3.500A) Processing helix chain 'D' and resid 2192 through 2221 removed outlier: 3.904A pdb=" N ARG D2200 " --> pdb=" O TRP D2196 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N THR D2202 " --> pdb=" O SER D2198 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU D2203 " --> pdb=" O ARG D2199 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP D2204 " --> pdb=" O ARG D2200 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D2205 " --> pdb=" O MET D2201 " (cutoff:3.500A) Processing helix chain 'D' and resid 2262 through 2304 removed outlier: 7.351A pdb=" N ILE D2278 " --> pdb=" O TYR D2274 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N GLY D2279 " --> pdb=" O TYR D2275 " (cutoff:3.500A) Proline residue: D2280 - end of helix Processing helix chain 'D' and resid 2319 through 2335 Processing helix chain 'D' and resid 2340 through 2345 Processing helix chain 'D' and resid 2348 through 2351 No H-bonds generated for 'chain 'D' and resid 2348 through 2351' Processing helix chain 'D' and resid 2353 through 2363 removed outlier: 3.767A pdb=" N VAL D2362 " --> pdb=" O VAL D2358 " (cutoff:3.500A) Processing helix chain 'D' and resid 2366 through 2390 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 2536 removed outlier: 4.186A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D2515 " --> pdb=" O LEU D2511 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE D2516 " --> pdb=" O ILE D2512 " (cutoff:3.500A) Processing helix chain 'D' and resid 2545 through 2548 Processing helix chain 'D' and resid 2565 through 2577 removed outlier: 3.550A pdb=" N LEU D2569 " --> pdb=" O MET D2565 " (cutoff:3.500A) 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 2596 Processing helix chain 'D' and resid 2608 through 2610 No H-bonds generated for 'chain 'D' and resid 2608 through 2610' Processing helix chain 'D' and resid 2629 through 2645 removed outlier: 3.956A pdb=" N UNK D2645 " --> pdb=" O UNK D2641 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 183 through 187 removed outlier: 3.912A pdb=" N SER A 120 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N SER A 15 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU A 223 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR A 17 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE A 221 " --> pdb=" O TYR A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= C, first strand: chain 'A' and resid 26 through 28 Processing sheet with id= D, first strand: chain 'A' and resid 194 through 196 Processing sheet with id= E, first strand: chain 'A' and resid 241 through 245 Processing sheet with id= F, first strand: chain 'A' and resid 251 through 257 removed outlier: 4.410A pdb=" N PHE A 251 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 283 through 287 Processing sheet with id= H, first strand: chain 'A' and resid 314 through 319 Processing sheet with id= I, first strand: chain 'A' and resid 367 through 371 Processing sheet with id= J, first strand: chain 'A' and resid 397 through 400 Processing sheet with id= K, first strand: chain 'A' and resid 667 through 669 Processing sheet with id= L, first strand: chain 'A' and resid 800 through 802 removed outlier: 6.392A pdb=" N GLN A1096 " --> pdb=" O ARG A 801 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'A' and resid 2121 through 2127 Processing sheet with id= N, first strand: chain 'A' and resid 2396 through 2398 Processing sheet with id= O, first strand: chain 'A' and resid 132 through 140 removed outlier: 3.662A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.918A pdb=" N SER B 120 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N SER B 15 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU B 223 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR B 17 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE B 221 " --> pdb=" O TYR B 17 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= R, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= S, first strand: chain 'B' and resid 194 through 196 Processing sheet with id= T, first strand: chain 'B' and resid 241 through 245 Processing sheet with id= U, first strand: chain 'B' and resid 251 through 257 removed outlier: 4.408A pdb=" N PHE B 251 " --> pdb=" O ARG B 266 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 283 through 287 Processing sheet with id= W, first strand: chain 'B' and resid 314 through 319 Processing sheet with id= X, first strand: chain 'B' and resid 367 through 371 Processing sheet with id= Y, first strand: chain 'B' and resid 397 through 400 Processing sheet with id= Z, first strand: chain 'B' and resid 667 through 669 Processing sheet with id= AA, first strand: chain 'B' and resid 800 through 802 removed outlier: 6.389A pdb=" N GLN B1096 " --> pdb=" O ARG B 801 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'B' and resid 2121 through 2127 Processing sheet with id= AC, first strand: chain 'B' and resid 2396 through 2398 Processing sheet with id= AD, first strand: chain 'B' and resid 132 through 140 removed outlier: 3.665A pdb=" N ARG B 149 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 183 through 187 removed outlier: 3.922A pdb=" N SER C 120 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER C 15 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU C 223 " --> pdb=" O SER C 15 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR C 17 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE C 221 " --> pdb=" O TYR C 17 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 17 through 19 Processing sheet with id= AG, first strand: chain 'C' and resid 26 through 28 Processing sheet with id= AH, first strand: chain 'C' and resid 194 through 196 Processing sheet with id= AI, first strand: chain 'C' and resid 241 through 245 Processing sheet with id= AJ, first strand: chain 'C' and resid 251 through 257 removed outlier: 4.427A pdb=" N PHE C 251 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 283 through 287 Processing sheet with id= AL, first strand: chain 'C' and resid 314 through 319 Processing sheet with id= AM, first strand: chain 'C' and resid 367 through 371 Processing sheet with id= AN, first strand: chain 'C' and resid 397 through 400 Processing sheet with id= AO, first strand: chain 'C' and resid 667 through 669 Processing sheet with id= AP, first strand: chain 'C' and resid 800 through 802 removed outlier: 6.409A pdb=" N GLN C1096 " --> pdb=" O ARG C 801 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'C' and resid 2121 through 2127 Processing sheet with id= AR, first strand: chain 'C' and resid 2396 through 2398 Processing sheet with id= AS, first strand: chain 'C' and resid 132 through 140 removed outlier: 3.662A pdb=" N ARG C 149 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'D' and resid 183 through 187 removed outlier: 3.916A pdb=" N SER D 120 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N SER D 15 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU D 223 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR D 17 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE D 221 " --> pdb=" O TYR D 17 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'D' and resid 17 through 19 Processing sheet with id= AV, first strand: chain 'D' and resid 26 through 28 Processing sheet with id= AW, first strand: chain 'D' and resid 194 through 196 Processing sheet with id= AX, first strand: chain 'D' and resid 241 through 245 Processing sheet with id= AY, first strand: chain 'D' and resid 251 through 257 removed outlier: 4.427A pdb=" N PHE D 251 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'D' and resid 283 through 287 Processing sheet with id= BA, first strand: chain 'D' and resid 314 through 319 Processing sheet with id= BB, first strand: chain 'D' and resid 367 through 371 Processing sheet with id= BC, first strand: chain 'D' and resid 397 through 400 Processing sheet with id= BD, first strand: chain 'D' and resid 667 through 669 Processing sheet with id= BE, first strand: chain 'D' and resid 800 through 802 removed outlier: 6.411A pdb=" N GLN D1096 " --> pdb=" O ARG D 801 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'D' and resid 2121 through 2127 Processing sheet with id= BG, first strand: chain 'D' and resid 2396 through 2398 Processing sheet with id= BH, first strand: chain 'D' and resid 132 through 140 removed outlier: 3.664A pdb=" N ARG D 149 " --> pdb=" O ASN D 136 " (cutoff:3.500A) 3618 hydrogen bonds defined for protein. 10458 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: 33.45 Time building geometry restraints manager: 25.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22475 1.34 - 1.46: 11424 1.46 - 1.58: 35437 1.58 - 1.70: 32 1.70 - 1.81: 660 Bond restraints: 70028 Sorted by residual: bond pdb=" O5 I3P A2702 " pdb=" P5 I3P A2702 " ideal model delta sigma weight residual 1.695 1.639 0.056 2.00e-02 2.50e+03 7.71e+00 bond pdb=" O5 I3P D2702 " pdb=" P5 I3P D2702 " ideal model delta sigma weight residual 1.695 1.640 0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" O5 I3P B2702 " pdb=" P5 I3P B2702 " ideal model delta sigma weight residual 1.695 1.640 0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" O5 I3P C2702 " pdb=" P5 I3P C2702 " ideal model delta sigma weight residual 1.695 1.640 0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" O4 I3P C2702 " pdb=" P4 I3P C2702 " ideal model delta sigma weight residual 1.697 1.645 0.052 2.00e-02 2.50e+03 6.85e+00 ... (remaining 70023 not shown) Histogram of bond angle deviations from ideal: 96.30 - 105.01: 832 105.01 - 113.73: 40971 113.73 - 122.44: 45607 122.44 - 131.16: 6943 131.16 - 139.87: 291 Bond angle restraints: 94644 Sorted by residual: angle pdb=" N LEU B1644 " pdb=" CA LEU B1644 " pdb=" C LEU B1644 " ideal model delta sigma weight residual 113.43 108.07 5.36 1.26e+00 6.30e-01 1.81e+01 angle pdb=" N LEU C1644 " pdb=" CA LEU C1644 " pdb=" C LEU C1644 " ideal model delta sigma weight residual 113.43 108.16 5.27 1.26e+00 6.30e-01 1.75e+01 angle pdb=" N LEU A1644 " pdb=" CA LEU A1644 " pdb=" C LEU A1644 " ideal model delta sigma weight residual 113.43 108.21 5.22 1.26e+00 6.30e-01 1.71e+01 angle pdb=" N LEU D1644 " pdb=" CA LEU D1644 " pdb=" C LEU D1644 " ideal model delta sigma weight residual 113.43 108.27 5.16 1.26e+00 6.30e-01 1.68e+01 angle pdb=" N ILE A2479 " pdb=" CA ILE A2479 " pdb=" C ILE A2479 " ideal model delta sigma weight residual 112.96 109.03 3.93 1.00e+00 1.00e+00 1.55e+01 ... (remaining 94639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 37979 17.68 - 35.36: 3619 35.36 - 53.04: 579 53.04 - 70.71: 74 70.71 - 88.39: 45 Dihedral angle restraints: 42296 sinusoidal: 17276 harmonic: 25020 Sorted by residual: dihedral pdb=" CA MET C1200 " pdb=" C MET C1200 " pdb=" N ASP C1201 " pdb=" CA ASP C1201 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA TRP B 696 " pdb=" C TRP B 696 " pdb=" N THR B 697 " pdb=" CA THR B 697 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA MET B1200 " pdb=" C MET B1200 " pdb=" N ASP B1201 " pdb=" CA ASP B1201 " ideal model delta harmonic sigma weight residual 180.00 157.84 22.16 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 42293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 9550 0.058 - 0.115: 1238 0.115 - 0.173: 76 0.173 - 0.230: 0 0.230 - 0.288: 12 Chirality restraints: 10876 Sorted by residual: chirality pdb=" C3' ATP C2703 " pdb=" C2' ATP C2703 " pdb=" C4' ATP C2703 " pdb=" O3' ATP C2703 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C3' ATP B2703 " pdb=" C2' ATP B2703 " pdb=" C4' ATP B2703 " pdb=" O3' ATP B2703 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C3' ATP A2703 " pdb=" C2' ATP A2703 " pdb=" C4' ATP A2703 " pdb=" O3' ATP A2703 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 10873 not shown) Planarity restraints: 11976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B1688 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C LYS B1688 " 0.034 2.00e-02 2.50e+03 pdb=" O LYS B1688 " -0.013 2.00e-02 2.50e+03 pdb=" N MET B1689 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B1986 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C MET B1986 " 0.034 2.00e-02 2.50e+03 pdb=" O MET B1986 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP B1987 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A1986 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C MET A1986 " 0.034 2.00e-02 2.50e+03 pdb=" O MET A1986 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A1987 " -0.012 2.00e-02 2.50e+03 ... (remaining 11973 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 869 2.61 - 3.18: 64451 3.18 - 3.75: 109667 3.75 - 4.33: 154865 4.33 - 4.90: 256291 Nonbonded interactions: 586143 Sorted by model distance: nonbonded pdb=" OG1 THR C 668 " pdb=" OH TYR C 729 " model vdw 2.035 2.440 nonbonded pdb=" OG1 THR B 668 " pdb=" OH TYR B 729 " model vdw 2.042 2.440 nonbonded pdb=" OG1 THR D 668 " pdb=" OH TYR D 729 " model vdw 2.048 2.440 nonbonded pdb=" OG1 THR A 668 " pdb=" OH TYR A 729 " model vdw 2.054 2.440 nonbonded pdb=" OH TYR B 17 " pdb=" OD1 ASP B 44 " model vdw 2.096 2.440 ... (remaining 586138 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.740 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: 0.050 Extract box with map and model: 25.510 Check model and map are aligned: 0.760 Set scattering table: 0.460 Process input model: 153.450 Find NCS groups from input model: 3.840 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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 : 0.004 0.056 70028 Z= 0.268 Angle : 0.540 7.562 94644 Z= 0.291 Chirality : 0.038 0.288 10876 Planarity : 0.003 0.054 11976 Dihedral : 13.703 88.394 25964 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.65 % Favored : 95.30 % Rotamer Outliers : 0.00 % 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: 1.52 (0.10), residues: 8276 helix: 2.11 (0.07), residues: 5268 sheet: -0.97 (0.19), residues: 640 loop : -0.95 (0.13), residues: 2368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1899 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1899 time to evaluate : 6.080 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 outliers start: 0 outliers final: 0 residues processed: 1899 average time/residue: 0.6867 time to fit residues: 2201.1793 Evaluate side-chains 930 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 930 time to evaluate : 6.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.4994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 719 optimal weight: 9.9990 chunk 645 optimal weight: 7.9990 chunk 358 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 435 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 chunk 667 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 406 optimal weight: 0.9980 chunk 497 optimal weight: 4.9990 chunk 773 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 491 GLN A1065 HIS A1168 ASN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1288 HIS A1304 HIS A1596 GLN ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN B 491 GLN B 641 ASN B1065 HIS B1168 ASN ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 HIS B1304 HIS B1380 ASN ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2135 GLN ** B2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2292 ASN C 23 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN C 395 ASN C 491 GLN ** C 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS C1168 ASN ** C1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 HIS C1293 HIS C1304 HIS C1670 GLN ** C1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2135 GLN ** C2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2292 ASN D 23 ASN D 214 ASN D 301 ASN D 395 ASN D1168 ASN ** D1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1288 HIS D1293 HIS D1304 HIS ** D1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 70028 Z= 0.273 Angle : 0.600 8.756 94644 Z= 0.307 Chirality : 0.041 0.187 10876 Planarity : 0.004 0.082 11976 Dihedral : 4.239 37.963 9128 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer Outliers : 1.46 % 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: 1.46 (0.10), residues: 8276 helix: 2.03 (0.07), residues: 5224 sheet: -0.68 (0.20), residues: 632 loop : -0.96 (0.13), residues: 2420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1121 time to evaluate : 6.183 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 outliers start: 111 outliers final: 62 residues processed: 1188 average time/residue: 0.6886 time to fit residues: 1436.7780 Evaluate side-chains 908 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 846 time to evaluate : 6.119 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.5247 time to fit residues: 70.6394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 429 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 643 optimal weight: 0.0050 chunk 526 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 chunk 775 optimal weight: 0.9980 chunk 837 optimal weight: 6.9990 chunk 690 optimal weight: 4.9990 chunk 768 optimal weight: 20.0000 chunk 264 optimal weight: 2.9990 chunk 621 optimal weight: 8.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 GLN A1065 HIS A1194 GLN ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 713 GLN B1065 HIS B1194 GLN ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 GLN ** B1895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN C 460 ASN C 466 GLN ** C 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS C1194 GLN C1199 ASN ** C1895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2135 GLN ** C2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN D 460 ASN D1065 HIS D1194 GLN ** D1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1939 GLN ** D1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2292 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 70028 Z= 0.335 Angle : 0.588 9.709 94644 Z= 0.303 Chirality : 0.041 0.185 10876 Planarity : 0.004 0.048 11976 Dihedral : 4.291 39.251 9128 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.02 % Favored : 95.94 % Rotamer Outliers : 1.59 % 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: 1.25 (0.09), residues: 8276 helix: 1.88 (0.07), residues: 5232 sheet: -0.77 (0.20), residues: 640 loop : -1.06 (0.13), residues: 2404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 955 time to evaluate : 6.178 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 outliers start: 121 outliers final: 59 residues processed: 1039 average time/residue: 0.6324 time to fit residues: 1157.0100 Evaluate side-chains 888 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 829 time to evaluate : 6.235 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.5102 time to fit residues: 66.2649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 765 optimal weight: 6.9990 chunk 582 optimal weight: 9.9990 chunk 402 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 369 optimal weight: 8.9990 chunk 520 optimal weight: 8.9990 chunk 777 optimal weight: 5.9990 chunk 823 optimal weight: 7.9990 chunk 406 optimal weight: 0.9990 chunk 737 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 HIS A1065 HIS ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1895 GLN A1955 ASN ** A1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2123 GLN A2135 GLN ** A2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 ASN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 HIS B1065 HIS ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1895 GLN B1955 ASN ** B1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2292 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS C1199 ASN ** C1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1895 GLN C1955 ASN ** C1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2292 ASN ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 GLN D1065 HIS ** D1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1670 GLN D1895 GLN D1955 ASN ** D1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2123 GLN D2135 GLN ** D2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.068 70028 Z= 0.565 Angle : 0.722 8.871 94644 Z= 0.369 Chirality : 0.046 0.158 10876 Planarity : 0.005 0.056 11976 Dihedral : 4.739 47.850 9128 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.97 % Rotamer Outliers : 2.42 % 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: 0.54 (0.09), residues: 8276 helix: 1.31 (0.07), residues: 5280 sheet: -0.97 (0.20), residues: 644 loop : -1.40 (0.13), residues: 2352 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 936 time to evaluate : 6.163 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 outliers start: 184 outliers final: 106 residues processed: 1063 average time/residue: 0.6575 time to fit residues: 1220.5555 Evaluate side-chains 941 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 835 time to evaluate : 6.183 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 0 residues processed: 106 average time/residue: 0.5434 time to fit residues: 115.9310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 685 optimal weight: 0.9980 chunk 467 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 613 optimal weight: 0.7980 chunk 339 optimal weight: 0.9980 chunk 702 optimal weight: 7.9990 chunk 569 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 420 optimal weight: 0.9980 chunk 739 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 HIS ** A1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2123 GLN A2135 GLN ** A2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2303 ASN B 301 ASN B1065 HIS ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 HIS ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** C 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1670 GLN ** D1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2123 GLN D2135 GLN ** D2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2292 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 70028 Z= 0.174 Angle : 0.528 12.051 94644 Z= 0.272 Chirality : 0.039 0.197 10876 Planarity : 0.003 0.039 11976 Dihedral : 4.301 48.498 9128 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer Outliers : 1.22 % 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: 0.99 (0.09), residues: 8276 helix: 1.67 (0.07), residues: 5268 sheet: -0.90 (0.20), residues: 636 loop : -1.19 (0.13), residues: 2372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 999 time to evaluate : 6.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 41 residues processed: 1055 average time/residue: 0.6323 time to fit residues: 1177.3371 Evaluate side-chains 914 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 873 time to evaluate : 6.134 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.5279 time to fit residues: 49.5866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 277 optimal weight: 0.8980 chunk 741 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 483 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 824 optimal weight: 1.9990 chunk 684 optimal weight: 0.5980 chunk 381 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 272 optimal weight: 8.9990 chunk 432 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 HIS A1402 HIS ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 ASN B 301 ASN B1065 HIS ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1402 HIS ** B1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2051 HIS ** B2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2292 ASN ** C 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2292 ASN ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1402 HIS ** D1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 70028 Z= 0.245 Angle : 0.556 13.136 94644 Z= 0.281 Chirality : 0.040 0.277 10876 Planarity : 0.003 0.051 11976 Dihedral : 4.241 47.765 9128 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.05 % Favored : 95.92 % Rotamer Outliers : 1.20 % 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: 1.00 (0.09), residues: 8276 helix: 1.69 (0.07), residues: 5260 sheet: -1.00 (0.20), residues: 636 loop : -1.18 (0.13), residues: 2380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 925 time to evaluate : 6.067 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 outliers start: 91 outliers final: 56 residues processed: 982 average time/residue: 0.6451 time to fit residues: 1115.6383 Evaluate side-chains 918 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 862 time to evaluate : 6.095 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.5538 time to fit residues: 66.4175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 794 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 469 optimal weight: 4.9990 chunk 601 optimal weight: 5.9990 chunk 466 optimal weight: 3.9990 chunk 693 optimal weight: 5.9990 chunk 460 optimal weight: 1.9990 chunk 821 optimal weight: 6.9990 chunk 513 optimal weight: 4.9990 chunk 500 optimal weight: 1.9990 chunk 379 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 HIS ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2303 ASN B1065 HIS ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 HIS ** B1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2051 HIS ** C2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1065 HIS ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2292 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 70028 Z= 0.389 Angle : 0.615 13.147 94644 Z= 0.313 Chirality : 0.042 0.310 10876 Planarity : 0.004 0.043 11976 Dihedral : 4.413 51.248 9128 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.54 % Favored : 95.42 % Rotamer Outliers : 0.97 % 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: 8276 helix: 1.54 (0.07), residues: 5256 sheet: -1.16 (0.20), residues: 624 loop : -1.31 (0.13), residues: 2396 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 906 time to evaluate : 6.075 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 outliers start: 74 outliers final: 44 residues processed: 944 average time/residue: 0.6435 time to fit residues: 1070.8849 Evaluate side-chains 896 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 852 time to evaluate : 6.172 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.5553 time to fit residues: 53.6101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 508 optimal weight: 10.0000 chunk 327 optimal weight: 0.0270 chunk 490 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 522 optimal weight: 10.0000 chunk 559 optimal weight: 6.9990 chunk 406 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 645 optimal weight: 6.9990 overall best weight: 2.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 HIS ** A1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 ASN B1065 HIS ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2292 ASN ** C 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2292 ASN D1065 HIS ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 70028 Z= 0.345 Angle : 0.603 17.478 94644 Z= 0.305 Chirality : 0.041 0.329 10876 Planarity : 0.004 0.043 11976 Dihedral : 4.435 53.770 9128 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer Outliers : 0.72 % 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: 0.70 (0.09), residues: 8276 helix: 1.49 (0.07), residues: 5260 sheet: -1.29 (0.19), residues: 648 loop : -1.33 (0.13), residues: 2368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 914 time to evaluate : 6.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 39 residues processed: 947 average time/residue: 0.6422 time to fit residues: 1076.9445 Evaluate side-chains 898 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 859 time to evaluate : 6.235 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.5195 time to fit residues: 47.3092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 747 optimal weight: 0.9990 chunk 786 optimal weight: 0.6980 chunk 717 optimal weight: 5.9990 chunk 765 optimal weight: 0.9980 chunk 460 optimal weight: 2.9990 chunk 333 optimal weight: 9.9990 chunk 600 optimal weight: 0.3980 chunk 234 optimal weight: 0.5980 chunk 691 optimal weight: 0.7980 chunk 723 optimal weight: 3.9990 chunk 762 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 HIS ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2051 HIS ** A2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1065 HIS ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 HIS ** B1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 GLN D1065 HIS D1193 GLN ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2051 HIS ** D2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2292 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 70028 Z= 0.172 Angle : 0.551 15.807 94644 Z= 0.277 Chirality : 0.039 0.389 10876 Planarity : 0.003 0.046 11976 Dihedral : 4.202 52.366 9128 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.50 % Favored : 96.48 % Rotamer Outliers : 0.25 % 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: 0.92 (0.10), residues: 8276 helix: 1.67 (0.07), residues: 5264 sheet: -1.27 (0.20), residues: 652 loop : -1.22 (0.13), residues: 2360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 946 time to evaluate : 6.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 955 average time/residue: 0.6665 time to fit residues: 1131.0267 Evaluate side-chains 897 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 885 time to evaluate : 6.134 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5304 time to fit residues: 20.7662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 502 optimal weight: 2.9990 chunk 809 optimal weight: 0.8980 chunk 493 optimal weight: 0.9980 chunk 383 optimal weight: 4.9990 chunk 562 optimal weight: 4.9990 chunk 848 optimal weight: 6.9990 chunk 781 optimal weight: 0.9980 chunk 675 optimal weight: 0.0270 chunk 70 optimal weight: 4.9990 chunk 522 optimal weight: 5.9990 chunk 414 optimal weight: 0.5980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 GLN A1065 HIS ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1065 HIS ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN D1065 HIS ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 70028 Z= 0.169 Angle : 0.557 17.755 94644 Z= 0.278 Chirality : 0.039 0.384 10876 Planarity : 0.003 0.046 11976 Dihedral : 4.104 51.149 9128 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.75 % Favored : 96.24 % 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: 0.99 (0.10), residues: 8276 helix: 1.72 (0.07), residues: 5240 sheet: -1.32 (0.19), residues: 684 loop : -1.12 (0.13), residues: 2352 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 929 time to evaluate : 6.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 934 average time/residue: 0.6846 time to fit residues: 1132.5366 Evaluate side-chains 885 residues out of total 7668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 881 time to evaluate : 6.132 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5681 time to fit residues: 14.3485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 852 random chunks: chunk 536 optimal weight: 7.9990 chunk 720 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 623 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 676 optimal weight: 0.9980 chunk 283 optimal weight: 8.9990 chunk 695 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN A1065 HIS ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS C1402 HIS ** C1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1065 HIS ** D1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.172651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132165 restraints weight = 99954.380| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.27 r_work: 0.3390 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 70028 Z= 0.287 Angle : 0.597 15.668 94644 Z= 0.300 Chirality : 0.041 0.378 10876 Planarity : 0.003 0.047 11976 Dihedral : 4.212 53.045 9128 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.39 % Favored : 95.60 % Rotamer Outliers : 0.28 % 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: 0.90 (0.09), residues: 8276 helix: 1.66 (0.07), residues: 5240 sheet: -1.34 (0.19), residues: 684 loop : -1.21 (0.13), residues: 2352 =============================================================================== Job complete usr+sys time: 19196.54 seconds wall clock time: 337 minutes 18.37 seconds (20238.37 seconds total)