Starting phenix.real_space_refine on Sun Mar 24 17:12:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rla_4917/03_2024/6rla_4917_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rla_4917/03_2024/6rla_4917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rla_4917/03_2024/6rla_4917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rla_4917/03_2024/6rla_4917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rla_4917/03_2024/6rla_4917_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rla_4917/03_2024/6rla_4917_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 P 18 5.49 5 Mg 2 5.21 5 S 196 5.16 5 C 27358 2.51 5 N 7370 2.21 5 O 8090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 1523": "NH1" <-> "NH2" Residue "A PHE 1740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1801": "NH1" <-> "NH2" Residue "A ARG 1867": "NH1" <-> "NH2" Residue "A TYR 2162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2270": "NH1" <-> "NH2" Residue "A ARG 2353": "NH1" <-> "NH2" Residue "A ARG 2426": "NH1" <-> "NH2" Residue "A ARG 2508": "NH1" <-> "NH2" Residue "A TYR 2685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3577": "NH1" <-> "NH2" Residue "A ARG 3860": "NH1" <-> "NH2" Residue "A ARG 4207": "NH1" <-> "NH2" Residue "B ARG 1523": "NH1" <-> "NH2" Residue "B PHE 1740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1801": "NH1" <-> "NH2" Residue "B ARG 1867": "NH1" <-> "NH2" Residue "B TYR 2162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2270": "NH1" <-> "NH2" Residue "B ARG 2353": "NH1" <-> "NH2" Residue "B ARG 2426": "NH1" <-> "NH2" Residue "B ARG 2508": "NH1" <-> "NH2" Residue "B TYR 2685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3577": "NH1" <-> "NH2" Residue "B ARG 3860": "NH1" <-> "NH2" Residue "B ARG 4207": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43034 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 21404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2750, 21404 Classifications: {'peptide': 2750} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 110, 'TRANS': 2635} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 633 Unresolved non-hydrogen angles: 778 Unresolved non-hydrogen dihedrals: 514 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 351 Chain: "B" Number of atoms: 21404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2750, 21404 Classifications: {'peptide': 2750} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 110, 'TRANS': 2635} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 633 Unresolved non-hydrogen angles: 778 Unresolved non-hydrogen dihedrals: 514 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 3, 'GLU:plan': 26, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 351 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 22.72, per 1000 atoms: 0.53 Number of scatterers: 43034 At special positions: 0 Unit cell: (137.61, 212.67, 190.43, 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) S 196 16.00 P 18 15.00 Mg 2 11.99 O 8090 8.00 N 7370 7.00 C 27358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.75 Conformation dependent library (CDL) restraints added in 8.4 seconds 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10412 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 222 helices and 40 sheets defined 51.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 20.33 Creating SS restraints... Processing helix chain 'A' and resid 1257 through 1272 removed outlier: 3.854A pdb=" N VAL A1272 " --> pdb=" O ASP A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1314 removed outlier: 3.885A pdb=" N GLN A1301 " --> pdb=" O ASP A1297 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A1314 " --> pdb=" O GLN A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1320 removed outlier: 4.441A pdb=" N LYS A1319 " --> pdb=" O PRO A1316 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A1320 " --> pdb=" O TYR A1317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1316 through 1320' Processing helix chain 'A' and resid 1322 through 1358 removed outlier: 3.856A pdb=" N GLU A1337 " --> pdb=" O ALA A1333 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N HIS A1344 " --> pdb=" O GLN A1340 " (cutoff:3.500A) Proline residue: A1354 - end of helix Processing helix chain 'A' and resid 1362 through 1384 removed outlier: 4.391A pdb=" N ARG A1367 " --> pdb=" O LYS A1363 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE A1378 " --> pdb=" O ASP A1374 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A1381 " --> pdb=" O SER A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1390 No H-bonds generated for 'chain 'A' and resid 1388 through 1390' Processing helix chain 'A' and resid 1397 through 1425 removed outlier: 5.360A pdb=" N GLU A1417 " --> pdb=" O ARG A1413 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE A1418 " --> pdb=" O SER A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1430 removed outlier: 3.997A pdb=" N TYR A1430 " --> pdb=" O PRO A1427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1427 through 1430' Processing helix chain 'A' and resid 1434 through 1442 removed outlier: 4.050A pdb=" N GLU A1439 " --> pdb=" O ASP A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1453 Processing helix chain 'A' and resid 1496 through 1522 removed outlier: 5.490A pdb=" N ASN A1501 " --> pdb=" O THR A1498 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A1505 " --> pdb=" O ASP A1502 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A1509 " --> pdb=" O GLU A1506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A1511 " --> pdb=" O LYS A1508 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A1515 " --> pdb=" O GLU A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1557 removed outlier: 3.741A pdb=" N LEU A1541 " --> pdb=" O GLN A1537 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS A1556 " --> pdb=" O GLU A1552 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1582 removed outlier: 3.965A pdb=" N THR A1579 " --> pdb=" O THR A1575 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A1580 " --> pdb=" O ASN A1576 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A1581 " --> pdb=" O ILE A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1594 through 1616 removed outlier: 3.605A pdb=" N LEU A1599 " --> pdb=" O LYS A1595 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A1601 " --> pdb=" O LYS A1597 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP A1602 " --> pdb=" O ALA A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1624 through 1627 No H-bonds generated for 'chain 'A' and resid 1624 through 1627' Processing helix chain 'A' and resid 1666 through 1680 removed outlier: 3.790A pdb=" N LYS A1670 " --> pdb=" O PRO A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1706 removed outlier: 3.684A pdb=" N VAL A1699 " --> pdb=" O LYS A1695 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A1700 " --> pdb=" O THR A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1734 removed outlier: 3.602A pdb=" N ILE A1727 " --> pdb=" O SER A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1748 through 1766 removed outlier: 3.670A pdb=" N MET A1756 " --> pdb=" O SER A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1806 through 1811 removed outlier: 3.561A pdb=" N LEU A1811 " --> pdb=" O ASN A1807 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1832 Processing helix chain 'A' and resid 1838 through 1855 removed outlier: 4.563A pdb=" N ARG A1843 " --> pdb=" O LYS A1839 " (cutoff:3.500A) Processing helix chain 'A' and resid 1866 through 1885 removed outlier: 3.567A pdb=" N ARG A1874 " --> pdb=" O LYS A1870 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A1879 " --> pdb=" O GLY A1875 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A1884 " --> pdb=" O LEU A1880 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A1885 " --> pdb=" O ARG A1881 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1908 removed outlier: 4.753A pdb=" N VAL A1898 " --> pdb=" O GLU A1894 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL A1899 " --> pdb=" O SER A1895 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN A1900 " --> pdb=" O HIS A1896 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN A1905 " --> pdb=" O ALA A1901 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET A1907 " --> pdb=" O ARG A1903 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER A1908 " --> pdb=" O LEU A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1925 Processing helix chain 'A' and resid 1938 through 1949 removed outlier: 3.679A pdb=" N ALA A1942 " --> pdb=" O GLU A1938 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1971 Processing helix chain 'A' and resid 1987 through 1997 removed outlier: 4.251A pdb=" N ALA A1994 " --> pdb=" O ARG A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2015 through 2018 No H-bonds generated for 'chain 'A' and resid 2015 through 2018' Processing helix chain 'A' and resid 2033 through 2043 Processing helix chain 'A' and resid 2060 through 2066 removed outlier: 5.140A pdb=" N SER A2065 " --> pdb=" O GLU A2061 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A2066 " --> pdb=" O TRP A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2104 through 2107 No H-bonds generated for 'chain 'A' and resid 2104 through 2107' Processing helix chain 'A' and resid 2123 through 2131 removed outlier: 4.614A pdb=" N SER A2128 " --> pdb=" O SER A2124 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP A2129 " --> pdb=" O LEU A2125 " (cutoff:3.500A) Processing helix chain 'A' and resid 2138 through 2159 removed outlier: 4.262A pdb=" N ASP A2147 " --> pdb=" O ASN A2143 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU A2150 " --> pdb=" O GLY A2146 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS A2151 " --> pdb=" O ASP A2147 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A2152 " --> pdb=" O TYR A2148 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A2156 " --> pdb=" O ALA A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2168 through 2176 Processing helix chain 'A' and resid 2185 through 2196 removed outlier: 3.712A pdb=" N ILE A2190 " --> pdb=" O ASP A2186 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2214 removed outlier: 4.119A pdb=" N LEU A2206 " --> pdb=" O MET A2202 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU A2207 " --> pdb=" O LYS A2203 " (cutoff:3.500A) Processing helix chain 'A' and resid 2266 through 2276 Processing helix chain 'A' and resid 2297 through 2306 Processing helix chain 'A' and resid 2324 through 2332 Processing helix chain 'A' and resid 2373 through 2384 Processing helix chain 'A' and resid 2419 through 2424 removed outlier: 3.765A pdb=" N ILE A2424 " --> pdb=" O ARG A2420 " (cutoff:3.500A) Processing helix chain 'A' and resid 2435 through 2450 removed outlier: 3.681A pdb=" N THR A2440 " --> pdb=" O GLU A2436 " (cutoff:3.500A) Proline residue: A2448 - end of helix Processing helix chain 'A' and resid 2464 through 2483 Processing helix chain 'A' and resid 2496 through 2507 removed outlier: 3.998A pdb=" N LEU A2506 " --> pdb=" O TRP A2502 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHE A2507 " --> pdb=" O VAL A2503 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2538 removed outlier: 4.021A pdb=" N ILE A2526 " --> pdb=" O TYR A2522 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP A2537 " --> pdb=" O ARG A2533 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS A2538 " --> pdb=" O LEU A2534 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2559 Processing helix chain 'A' and resid 2604 through 2620 Processing helix chain 'A' and resid 2631 through 2644 removed outlier: 3.662A pdb=" N VAL A2643 " --> pdb=" O ARG A2639 " (cutoff:3.500A) Processing helix chain 'A' and resid 2662 through 2671 Processing helix chain 'A' and resid 2688 through 2703 Processing helix chain 'A' and resid 2714 through 2716 No H-bonds generated for 'chain 'A' and resid 2714 through 2716' Processing helix chain 'A' and resid 2722 through 2731 Processing helix chain 'A' and resid 2742 through 2758 Proline residue: A2746 - end of helix Proline residue: A2750 - end of helix removed outlier: 5.324A pdb=" N ASP A2753 " --> pdb=" O LEU A2749 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLN A2754 " --> pdb=" O PRO A2750 " (cutoff:3.500A) Processing helix chain 'A' and resid 2764 through 2774 Processing helix chain 'A' and resid 2787 through 2789 No H-bonds generated for 'chain 'A' and resid 2787 through 2789' Processing helix chain 'A' and resid 2791 through 2794 No H-bonds generated for 'chain 'A' and resid 2791 through 2794' Processing helix chain 'A' and resid 2797 through 2800 Processing helix chain 'A' and resid 2813 through 2822 removed outlier: 3.617A pdb=" N LYS A2817 " --> pdb=" O ASN A2813 " (cutoff:3.500A) Proline residue: A2820 - end of helix Processing helix chain 'A' and resid 2848 through 2865 removed outlier: 3.621A pdb=" N LEU A2852 " --> pdb=" O ASP A2848 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA A2864 " --> pdb=" O GLU A2860 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TYR A2865 " --> pdb=" O SER A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2869 through 2911 removed outlier: 3.584A pdb=" N ASN A2905 " --> pdb=" O VAL A2901 " (cutoff:3.500A) Processing helix chain 'A' and resid 2914 through 2924 Processing helix chain 'A' and resid 3169 through 3186 removed outlier: 3.648A pdb=" N GLN A3178 " --> pdb=" O VAL A3174 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ARG A3181 " --> pdb=" O ASN A3177 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A3184 " --> pdb=" O ASP A3180 " (cutoff:3.500A) Processing helix chain 'A' and resid 3189 through 3196 Processing helix chain 'A' and resid 3200 through 3213 removed outlier: 3.570A pdb=" N ILE A3211 " --> pdb=" O ALA A3207 " (cutoff:3.500A) Processing helix chain 'A' and resid 3219 through 3233 Processing helix chain 'A' and resid 3241 through 3244 No H-bonds generated for 'chain 'A' and resid 3241 through 3244' Processing helix chain 'A' and resid 3247 through 3254 Processing helix chain 'A' and resid 3262 through 3272 removed outlier: 3.501A pdb=" N ILE A3271 " --> pdb=" O ASN A3267 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A3272 " --> pdb=" O ALA A3268 " (cutoff:3.500A) Processing helix chain 'A' and resid 3286 through 3294 Processing helix chain 'A' and resid 3310 through 3319 Processing helix chain 'A' and resid 3335 through 3340 Proline residue: A3338 - end of helix No H-bonds generated for 'chain 'A' and resid 3335 through 3340' Processing helix chain 'A' and resid 3396 through 3411 removed outlier: 3.596A pdb=" N GLY A3401 " --> pdb=" O SER A3397 " (cutoff:3.500A) Processing helix chain 'A' and resid 3413 through 3445 removed outlier: 3.563A pdb=" N LEU A3423 " --> pdb=" O LYS A3419 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A3439 " --> pdb=" O LYS A3435 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU A3440 " --> pdb=" O LEU A3436 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU A3441 " --> pdb=" O GLU A3437 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU A3442 " --> pdb=" O GLU A3438 " (cutoff:3.500A) Processing helix chain 'A' and resid 3456 through 3489 removed outlier: 3.509A pdb=" N ASN A3462 " --> pdb=" O ILE A3458 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A3482 " --> pdb=" O SER A3478 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE A3483 " --> pdb=" O TYR A3479 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU A3488 " --> pdb=" O SER A3484 " (cutoff:3.500A) Processing helix chain 'A' and resid 3493 through 3511 removed outlier: 4.307A pdb=" N SER A3498 " --> pdb=" O PRO A3494 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR A3503 " --> pdb=" O ALA A3499 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A3504 " --> pdb=" O SER A3500 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP A3508 " --> pdb=" O PHE A3504 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU A3509 " --> pdb=" O ILE A3505 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER A3510 " --> pdb=" O ILE A3506 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LYS A3511 " --> pdb=" O SER A3507 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3532 removed outlier: 3.869A pdb=" N LEU A3531 " --> pdb=" O PHE A3527 " (cutoff:3.500A) Processing helix chain 'A' and resid 3541 through 3560 removed outlier: 4.501A pdb=" N GLN A3545 " --> pdb=" O GLU A3541 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A3546 " --> pdb=" O GLN A3542 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS A3553 " --> pdb=" O SER A3549 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET A3554 " --> pdb=" O SER A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3568 through 3579 Processing helix chain 'A' and resid 3589 through 3592 No H-bonds generated for 'chain 'A' and resid 3589 through 3592' Processing helix chain 'A' and resid 3620 through 3632 removed outlier: 4.209A pdb=" N ALA A3625 " --> pdb=" O GLU A3621 " (cutoff:3.500A) Processing helix chain 'A' and resid 3634 through 3640 Processing helix chain 'A' and resid 3647 through 3653 removed outlier: 3.781A pdb=" N ASN A3653 " --> pdb=" O ARG A3649 " (cutoff:3.500A) Processing helix chain 'A' and resid 3663 through 3665 No H-bonds generated for 'chain 'A' and resid 3663 through 3665' Processing helix chain 'A' and resid 3671 through 3681 removed outlier: 3.773A pdb=" N ILE A3675 " --> pdb=" O LEU A3671 " (cutoff:3.500A) Processing helix chain 'A' and resid 3686 through 3698 Processing helix chain 'A' and resid 3734 through 3744 Processing helix chain 'A' and resid 3760 through 3773 removed outlier: 3.891A pdb=" N GLN A3765 " --> pdb=" O ASP A3761 " (cutoff:3.500A) Processing helix chain 'A' and resid 3789 through 3798 Processing helix chain 'A' and resid 3819 through 3823 Processing helix chain 'A' and resid 3836 through 3846 Processing helix chain 'A' and resid 3849 through 3852 No H-bonds generated for 'chain 'A' and resid 3849 through 3852' Processing helix chain 'A' and resid 3858 through 3879 removed outlier: 4.220A pdb=" N HIS A3862 " --> pdb=" O THR A3858 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA A3863 " --> pdb=" O HIS A3859 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG A3878 " --> pdb=" O CYS A3874 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN A3879 " --> pdb=" O GLN A3875 " (cutoff:3.500A) Processing helix chain 'A' and resid 3893 through 3907 Processing helix chain 'A' and resid 3915 through 3925 removed outlier: 3.617A pdb=" N HIS A3919 " --> pdb=" O TRP A3915 " (cutoff:3.500A) Processing helix chain 'A' and resid 3928 through 3930 No H-bonds generated for 'chain 'A' and resid 3928 through 3930' Processing helix chain 'A' and resid 3934 through 3946 Processing helix chain 'A' and resid 3977 through 3986 removed outlier: 3.962A pdb=" N ILE A3984 " --> pdb=" O TYR A3980 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A3985 " --> pdb=" O ARG A3981 " (cutoff:3.500A) Processing helix chain 'A' and resid 3993 through 3995 No H-bonds generated for 'chain 'A' and resid 3993 through 3995' Processing helix chain 'A' and resid 4001 through 4022 removed outlier: 3.525A pdb=" N LEU A4021 " --> pdb=" O GLN A4017 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A4022 " --> pdb=" O LEU A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4033 through 4036 No H-bonds generated for 'chain 'A' and resid 4033 through 4036' Processing helix chain 'A' and resid 4041 through 4050 Processing helix chain 'A' and resid 4073 through 4099 removed outlier: 3.921A pdb=" N LEU A4097 " --> pdb=" O SER A4093 " (cutoff:3.500A) Processing helix chain 'A' and resid 4110 through 4119 Processing helix chain 'A' and resid 4125 through 4130 removed outlier: 3.845A pdb=" N LYS A4130 " --> pdb=" O ALA A4126 " (cutoff:3.500A) Processing helix chain 'A' and resid 4137 through 4158 removed outlier: 4.049A pdb=" N GLN A4152 " --> pdb=" O ALA A4148 " (cutoff:3.500A) Processing helix chain 'A' and resid 4170 through 4172 No H-bonds generated for 'chain 'A' and resid 4170 through 4172' Processing helix chain 'A' and resid 4176 through 4191 Processing helix chain 'A' and resid 4195 through 4197 No H-bonds generated for 'chain 'A' and resid 4195 through 4197' Processing helix chain 'A' and resid 4263 through 4265 No H-bonds generated for 'chain 'A' and resid 4263 through 4265' Processing helix chain 'A' and resid 4293 through 4297 Processing helix chain 'B' and resid 1257 through 1272 removed outlier: 3.853A pdb=" N VAL B1272 " --> pdb=" O ASP B1268 " (cutoff:3.500A) Processing helix chain 'B' and resid 1295 through 1314 removed outlier: 3.885A pdb=" N GLN B1301 " --> pdb=" O ASP B1297 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP B1314 " --> pdb=" O GLN B1310 " (cutoff:3.500A) Processing helix chain 'B' and resid 1316 through 1320 removed outlier: 4.442A pdb=" N LYS B1319 " --> pdb=" O PRO B1316 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B1320 " --> pdb=" O TYR B1317 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1316 through 1320' Processing helix chain 'B' and resid 1322 through 1358 removed outlier: 3.856A pdb=" N GLU B1337 " --> pdb=" O ALA B1333 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS B1344 " --> pdb=" O GLN B1340 " (cutoff:3.500A) Proline residue: B1354 - end of helix Processing helix chain 'B' and resid 1362 through 1384 removed outlier: 4.390A pdb=" N ARG B1367 " --> pdb=" O LYS B1363 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B1378 " --> pdb=" O ASP B1374 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B1381 " --> pdb=" O SER B1377 " (cutoff:3.500A) Processing helix chain 'B' and resid 1388 through 1390 No H-bonds generated for 'chain 'B' and resid 1388 through 1390' Processing helix chain 'B' and resid 1397 through 1425 removed outlier: 5.360A pdb=" N GLU B1417 " --> pdb=" O ARG B1413 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE B1418 " --> pdb=" O SER B1414 " (cutoff:3.500A) Processing helix chain 'B' and resid 1427 through 1430 removed outlier: 3.996A pdb=" N TYR B1430 " --> pdb=" O PRO B1427 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1427 through 1430' Processing helix chain 'B' and resid 1434 through 1442 removed outlier: 4.049A pdb=" N GLU B1439 " --> pdb=" O ASP B1435 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1453 Processing helix chain 'B' and resid 1496 through 1522 removed outlier: 5.491A pdb=" N ASN B1501 " --> pdb=" O THR B1498 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B1505 " --> pdb=" O ASP B1502 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B1509 " --> pdb=" O GLU B1506 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B1511 " --> pdb=" O LYS B1508 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B1515 " --> pdb=" O GLU B1512 " (cutoff:3.500A) Processing helix chain 'B' and resid 1536 through 1557 removed outlier: 3.741A pdb=" N LEU B1541 " --> pdb=" O GLN B1537 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B1556 " --> pdb=" O GLU B1552 " (cutoff:3.500A) Processing helix chain 'B' and resid 1561 through 1582 removed outlier: 3.965A pdb=" N THR B1579 " --> pdb=" O THR B1575 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER B1580 " --> pdb=" O ASN B1576 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B1581 " --> pdb=" O ILE B1577 " (cutoff:3.500A) Processing helix chain 'B' and resid 1594 through 1616 removed outlier: 3.606A pdb=" N LEU B1599 " --> pdb=" O LYS B1595 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU B1601 " --> pdb=" O LYS B1597 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP B1602 " --> pdb=" O ALA B1598 " (cutoff:3.500A) Processing helix chain 'B' and resid 1624 through 1627 No H-bonds generated for 'chain 'B' and resid 1624 through 1627' Processing helix chain 'B' and resid 1666 through 1680 removed outlier: 3.789A pdb=" N LYS B1670 " --> pdb=" O PRO B1666 " (cutoff:3.500A) Processing helix chain 'B' and resid 1695 through 1706 removed outlier: 3.684A pdb=" N VAL B1699 " --> pdb=" O LYS B1695 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS B1700 " --> pdb=" O THR B1696 " (cutoff:3.500A) Processing helix chain 'B' and resid 1721 through 1734 removed outlier: 3.602A pdb=" N ILE B1727 " --> pdb=" O SER B1723 " (cutoff:3.500A) Processing helix chain 'B' and resid 1748 through 1766 removed outlier: 3.671A pdb=" N MET B1756 " --> pdb=" O SER B1752 " (cutoff:3.500A) Processing helix chain 'B' and resid 1806 through 1811 removed outlier: 3.560A pdb=" N LEU B1811 " --> pdb=" O ASN B1807 " (cutoff:3.500A) Processing helix chain 'B' and resid 1823 through 1832 Processing helix chain 'B' and resid 1838 through 1855 removed outlier: 4.562A pdb=" N ARG B1843 " --> pdb=" O LYS B1839 " (cutoff:3.500A) Processing helix chain 'B' and resid 1866 through 1885 removed outlier: 3.568A pdb=" N ARG B1874 " --> pdb=" O LYS B1870 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B1879 " --> pdb=" O GLY B1875 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN B1884 " --> pdb=" O LEU B1880 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS B1885 " --> pdb=" O ARG B1881 " (cutoff:3.500A) Processing helix chain 'B' and resid 1892 through 1908 removed outlier: 4.753A pdb=" N VAL B1898 " --> pdb=" O GLU B1894 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL B1899 " --> pdb=" O SER B1895 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN B1900 " --> pdb=" O HIS B1896 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN B1905 " --> pdb=" O ALA B1901 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B1907 " --> pdb=" O ARG B1903 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER B1908 " --> pdb=" O LEU B1904 " (cutoff:3.500A) Processing helix chain 'B' and resid 1912 through 1925 Processing helix chain 'B' and resid 1938 through 1949 removed outlier: 3.679A pdb=" N ALA B1942 " --> pdb=" O GLU B1938 " (cutoff:3.500A) Processing helix chain 'B' and resid 1956 through 1971 Processing helix chain 'B' and resid 1987 through 1997 removed outlier: 4.251A pdb=" N ALA B1994 " --> pdb=" O ARG B1990 " (cutoff:3.500A) Processing helix chain 'B' and resid 2015 through 2018 No H-bonds generated for 'chain 'B' and resid 2015 through 2018' Processing helix chain 'B' and resid 2033 through 2043 Processing helix chain 'B' and resid 2060 through 2066 removed outlier: 5.139A pdb=" N SER B2065 " --> pdb=" O GLU B2061 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU B2066 " --> pdb=" O TRP B2062 " (cutoff:3.500A) Processing helix chain 'B' and resid 2104 through 2107 No H-bonds generated for 'chain 'B' and resid 2104 through 2107' Processing helix chain 'B' and resid 2123 through 2131 removed outlier: 4.614A pdb=" N SER B2128 " --> pdb=" O SER B2124 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP B2129 " --> pdb=" O LEU B2125 " (cutoff:3.500A) Processing helix chain 'B' and resid 2138 through 2159 removed outlier: 4.262A pdb=" N ASP B2147 " --> pdb=" O ASN B2143 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU B2150 " --> pdb=" O GLY B2146 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS B2151 " --> pdb=" O ASP B2147 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B2152 " --> pdb=" O TYR B2148 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B2156 " --> pdb=" O ALA B2152 " (cutoff:3.500A) Processing helix chain 'B' and resid 2168 through 2176 Processing helix chain 'B' and resid 2185 through 2196 removed outlier: 3.712A pdb=" N ILE B2190 " --> pdb=" O ASP B2186 " (cutoff:3.500A) Processing helix chain 'B' and resid 2202 through 2214 removed outlier: 4.118A pdb=" N LEU B2206 " --> pdb=" O MET B2202 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU B2207 " --> pdb=" O LYS B2203 " (cutoff:3.500A) Processing helix chain 'B' and resid 2266 through 2276 Processing helix chain 'B' and resid 2297 through 2306 Processing helix chain 'B' and resid 2324 through 2332 Processing helix chain 'B' and resid 2373 through 2384 Processing helix chain 'B' and resid 2419 through 2424 removed outlier: 3.765A pdb=" N ILE B2424 " --> pdb=" O ARG B2420 " (cutoff:3.500A) Processing helix chain 'B' and resid 2435 through 2450 removed outlier: 3.681A pdb=" N THR B2440 " --> pdb=" O GLU B2436 " (cutoff:3.500A) Proline residue: B2448 - end of helix Processing helix chain 'B' and resid 2464 through 2483 Processing helix chain 'B' and resid 2496 through 2507 removed outlier: 3.999A pdb=" N LEU B2506 " --> pdb=" O TRP B2502 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHE B2507 " --> pdb=" O VAL B2503 " (cutoff:3.500A) Processing helix chain 'B' and resid 2520 through 2538 removed outlier: 4.021A pdb=" N ILE B2526 " --> pdb=" O TYR B2522 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP B2537 " --> pdb=" O ARG B2533 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS B2538 " --> pdb=" O LEU B2534 " (cutoff:3.500A) Processing helix chain 'B' and resid 2542 through 2559 Processing helix chain 'B' and resid 2604 through 2620 Processing helix chain 'B' and resid 2631 through 2644 removed outlier: 3.662A pdb=" N VAL B2643 " --> pdb=" O ARG B2639 " (cutoff:3.500A) Processing helix chain 'B' and resid 2662 through 2671 Processing helix chain 'B' and resid 2688 through 2703 Processing helix chain 'B' and resid 2714 through 2716 No H-bonds generated for 'chain 'B' and resid 2714 through 2716' Processing helix chain 'B' and resid 2722 through 2731 Processing helix chain 'B' and resid 2742 through 2758 Proline residue: B2746 - end of helix Proline residue: B2750 - end of helix removed outlier: 5.324A pdb=" N ASP B2753 " --> pdb=" O LEU B2749 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLN B2754 " --> pdb=" O PRO B2750 " (cutoff:3.500A) Processing helix chain 'B' and resid 2764 through 2774 Processing helix chain 'B' and resid 2787 through 2789 No H-bonds generated for 'chain 'B' and resid 2787 through 2789' Processing helix chain 'B' and resid 2791 through 2794 No H-bonds generated for 'chain 'B' and resid 2791 through 2794' Processing helix chain 'B' and resid 2797 through 2800 Processing helix chain 'B' and resid 2813 through 2822 removed outlier: 3.617A pdb=" N LYS B2817 " --> pdb=" O ASN B2813 " (cutoff:3.500A) Proline residue: B2820 - end of helix Processing helix chain 'B' and resid 2848 through 2865 removed outlier: 3.621A pdb=" N LEU B2852 " --> pdb=" O ASP B2848 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA B2864 " --> pdb=" O GLU B2860 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N TYR B2865 " --> pdb=" O SER B2861 " (cutoff:3.500A) Processing helix chain 'B' and resid 2869 through 2911 removed outlier: 3.584A pdb=" N ASN B2905 " --> pdb=" O VAL B2901 " (cutoff:3.500A) Processing helix chain 'B' and resid 2914 through 2924 Processing helix chain 'B' and resid 3169 through 3186 removed outlier: 3.648A pdb=" N GLN B3178 " --> pdb=" O VAL B3174 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ARG B3181 " --> pdb=" O ASN B3177 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS B3184 " --> pdb=" O ASP B3180 " (cutoff:3.500A) Processing helix chain 'B' and resid 3189 through 3196 Processing helix chain 'B' and resid 3200 through 3213 removed outlier: 3.570A pdb=" N ILE B3211 " --> pdb=" O ALA B3207 " (cutoff:3.500A) Processing helix chain 'B' and resid 3219 through 3233 Processing helix chain 'B' and resid 3241 through 3244 No H-bonds generated for 'chain 'B' and resid 3241 through 3244' Processing helix chain 'B' and resid 3247 through 3254 Processing helix chain 'B' and resid 3262 through 3272 removed outlier: 3.501A pdb=" N ILE B3271 " --> pdb=" O ASN B3267 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B3272 " --> pdb=" O ALA B3268 " (cutoff:3.500A) Processing helix chain 'B' and resid 3286 through 3294 Processing helix chain 'B' and resid 3310 through 3319 Processing helix chain 'B' and resid 3335 through 3340 Proline residue: B3338 - end of helix No H-bonds generated for 'chain 'B' and resid 3335 through 3340' Processing helix chain 'B' and resid 3396 through 3411 removed outlier: 3.597A pdb=" N GLY B3401 " --> pdb=" O SER B3397 " (cutoff:3.500A) Processing helix chain 'B' and resid 3413 through 3445 removed outlier: 3.564A pdb=" N LEU B3423 " --> pdb=" O LYS B3419 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B3439 " --> pdb=" O LYS B3435 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU B3440 " --> pdb=" O LEU B3436 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU B3441 " --> pdb=" O GLU B3437 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU B3442 " --> pdb=" O GLU B3438 " (cutoff:3.500A) Processing helix chain 'B' and resid 3456 through 3489 removed outlier: 3.510A pdb=" N ASN B3462 " --> pdb=" O ILE B3458 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B3482 " --> pdb=" O SER B3478 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE B3483 " --> pdb=" O TYR B3479 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER B3484 " --> pdb=" O LYS B3480 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B3488 " --> pdb=" O SER B3484 " (cutoff:3.500A) Processing helix chain 'B' and resid 3493 through 3511 removed outlier: 4.306A pdb=" N SER B3498 " --> pdb=" O PRO B3494 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR B3503 " --> pdb=" O ALA B3499 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE B3504 " --> pdb=" O SER B3500 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP B3508 " --> pdb=" O PHE B3504 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU B3509 " --> pdb=" O ILE B3505 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER B3510 " --> pdb=" O ILE B3506 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LYS B3511 " --> pdb=" O SER B3507 " (cutoff:3.500A) Processing helix chain 'B' and resid 3521 through 3532 removed outlier: 3.869A pdb=" N LEU B3531 " --> pdb=" O PHE B3527 " (cutoff:3.500A) Processing helix chain 'B' and resid 3541 through 3560 removed outlier: 4.501A pdb=" N GLN B3545 " --> pdb=" O GLU B3541 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B3546 " --> pdb=" O GLN B3542 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B3553 " --> pdb=" O SER B3549 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET B3554 " --> pdb=" O SER B3550 " (cutoff:3.500A) Processing helix chain 'B' and resid 3568 through 3579 Processing helix chain 'B' and resid 3589 through 3592 No H-bonds generated for 'chain 'B' and resid 3589 through 3592' Processing helix chain 'B' and resid 3620 through 3632 removed outlier: 4.210A pdb=" N ALA B3625 " --> pdb=" O GLU B3621 " (cutoff:3.500A) Processing helix chain 'B' and resid 3634 through 3640 Processing helix chain 'B' and resid 3647 through 3653 removed outlier: 3.780A pdb=" N ASN B3653 " --> pdb=" O ARG B3649 " (cutoff:3.500A) Processing helix chain 'B' and resid 3663 through 3665 No H-bonds generated for 'chain 'B' and resid 3663 through 3665' Processing helix chain 'B' and resid 3671 through 3681 removed outlier: 3.772A pdb=" N ILE B3675 " --> pdb=" O LEU B3671 " (cutoff:3.500A) Processing helix chain 'B' and resid 3686 through 3698 Processing helix chain 'B' and resid 3734 through 3744 Processing helix chain 'B' and resid 3760 through 3773 removed outlier: 3.892A pdb=" N GLN B3765 " --> pdb=" O ASP B3761 " (cutoff:3.500A) Processing helix chain 'B' and resid 3789 through 3798 Processing helix chain 'B' and resid 3819 through 3823 Processing helix chain 'B' and resid 3836 through 3846 Processing helix chain 'B' and resid 3849 through 3852 No H-bonds generated for 'chain 'B' and resid 3849 through 3852' Processing helix chain 'B' and resid 3858 through 3879 removed outlier: 4.219A pdb=" N HIS B3862 " --> pdb=" O THR B3858 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B3863 " --> pdb=" O HIS B3859 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG B3878 " --> pdb=" O CYS B3874 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN B3879 " --> pdb=" O GLN B3875 " (cutoff:3.500A) Processing helix chain 'B' and resid 3893 through 3907 Processing helix chain 'B' and resid 3915 through 3925 removed outlier: 3.618A pdb=" N HIS B3919 " --> pdb=" O TRP B3915 " (cutoff:3.500A) Processing helix chain 'B' and resid 3928 through 3930 No H-bonds generated for 'chain 'B' and resid 3928 through 3930' Processing helix chain 'B' and resid 3934 through 3946 Processing helix chain 'B' and resid 3977 through 3986 removed outlier: 3.963A pdb=" N ILE B3984 " --> pdb=" O TYR B3980 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B3985 " --> pdb=" O ARG B3981 " (cutoff:3.500A) Processing helix chain 'B' and resid 3993 through 3995 No H-bonds generated for 'chain 'B' and resid 3993 through 3995' Processing helix chain 'B' and resid 4001 through 4022 removed outlier: 3.525A pdb=" N LEU B4021 " --> pdb=" O GLN B4017 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B4022 " --> pdb=" O LEU B4018 " (cutoff:3.500A) Processing helix chain 'B' and resid 4033 through 4036 No H-bonds generated for 'chain 'B' and resid 4033 through 4036' Processing helix chain 'B' and resid 4041 through 4050 Processing helix chain 'B' and resid 4073 through 4099 removed outlier: 3.921A pdb=" N LEU B4097 " --> pdb=" O SER B4093 " (cutoff:3.500A) Processing helix chain 'B' and resid 4110 through 4119 Processing helix chain 'B' and resid 4125 through 4130 removed outlier: 3.846A pdb=" N LYS B4130 " --> pdb=" O ALA B4126 " (cutoff:3.500A) Processing helix chain 'B' and resid 4137 through 4158 removed outlier: 4.049A pdb=" N GLN B4152 " --> pdb=" O ALA B4148 " (cutoff:3.500A) Processing helix chain 'B' and resid 4170 through 4172 No H-bonds generated for 'chain 'B' and resid 4170 through 4172' Processing helix chain 'B' and resid 4176 through 4191 Processing helix chain 'B' and resid 4195 through 4197 No H-bonds generated for 'chain 'B' and resid 4195 through 4197' Processing helix chain 'B' and resid 4263 through 4265 No H-bonds generated for 'chain 'B' and resid 4263 through 4265' Processing helix chain 'B' and resid 4293 through 4297 Processing sheet with id= A, first strand: chain 'A' and resid 1278 through 1281 Processing sheet with id= B, first strand: chain 'A' and resid 1631 through 1634 removed outlier: 3.682A pdb=" N TYR A1633 " --> pdb=" O CYS A1641 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A1641 " --> pdb=" O TYR A1633 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1686 through 1688 Processing sheet with id= D, first strand: chain 'A' and resid 1710 through 1712 removed outlier: 6.443A pdb=" N TRP A1737 " --> pdb=" O LEU A1711 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 2111 through 2113 removed outlier: 6.841A pdb=" N PHE A2092 " --> pdb=" O VAL A1975 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE A1977 " --> pdb=" O PHE A2092 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N PHE A2094 " --> pdb=" O ILE A1977 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A2095 " --> pdb=" O CYS A2054 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 2021 through 2023 removed outlier: 3.764A pdb=" N HIS A2021 " --> pdb=" O SER A2030 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU A2028 " --> pdb=" O ASP A2023 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 2075 through 2077 Processing sheet with id= H, first strand: chain 'A' and resid 2426 through 2429 removed outlier: 7.303A pdb=" N ALA A2404 " --> pdb=" O LEU A2289 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N GLY A2291 " --> pdb=" O ALA A2404 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N MET A2406 " --> pdb=" O GLY A2291 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2311 through 2316 removed outlier: 7.162A pdb=" N ARG A2353 " --> pdb=" O GLN A2312 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ALA A2314 " --> pdb=" O ARG A2353 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A2355 " --> pdb=" O ALA A2314 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL A2316 " --> pdb=" O VAL A2355 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TYR A2357 " --> pdb=" O VAL A2316 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 2335 through 2338 removed outlier: 3.506A pdb=" N VAL A2345 " --> pdb=" O ILE A2338 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 2386 through 2389 removed outlier: 3.720A pdb=" N GLU A2393 " --> pdb=" O ASP A2389 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 2804 through 2807 removed outlier: 6.485A pdb=" N ILE A2778 " --> pdb=" O LEU A2651 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU A2653 " --> pdb=" O ILE A2778 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A2780 " --> pdb=" O LEU A2653 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLY A2655 " --> pdb=" O LEU A2780 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N MET A2782 " --> pdb=" O GLY A2655 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL A2675 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A2711 " --> pdb=" O VAL A2675 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE A2677 " --> pdb=" O LEU A2711 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 3387 through 3391 removed outlier: 6.019A pdb=" N CYS A3277 " --> pdb=" O THR A3388 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL A3390 " --> pdb=" O CYS A3277 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE A3279 " --> pdb=" O VAL A3390 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU A3368 " --> pdb=" O PRO A3278 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N LEU A3280 " --> pdb=" O LEU A3368 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A3370 " --> pdb=" O LEU A3280 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A3301 " --> pdb=" O THR A3323 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 3345 through 3347 removed outlier: 3.559A pdb=" N ARG A3350 " --> pdb=" O GLN A3347 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A3355 " --> pdb=" O LYS A3358 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 3722 through 3726 Processing sheet with id= P, first strand: chain 'A' and resid 3752 through 3754 removed outlier: 6.235A pdb=" N CYS A3778 " --> pdb=" O VAL A3753 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'A' and resid 4198 through 4203 removed outlier: 3.930A pdb=" N VAL A4201 " --> pdb=" O GLY A4251 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A4251 " --> pdb=" O VAL A4201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A4203 " --> pdb=" O PHE A4249 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A4249 " --> pdb=" O SER A4203 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 4221 through 4223 removed outlier: 3.850A pdb=" N GLU A4223 " --> pdb=" O ALA A4301 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 4226 through 4228 Processing sheet with id= T, first strand: chain 'A' and resid 4266 through 4270 Processing sheet with id= U, first strand: chain 'B' and resid 1278 through 1281 Processing sheet with id= V, first strand: chain 'B' and resid 1631 through 1634 removed outlier: 3.682A pdb=" N TYR B1633 " --> pdb=" O CYS B1641 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS B1641 " --> pdb=" O TYR B1633 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 1686 through 1688 Processing sheet with id= X, first strand: chain 'B' and resid 1710 through 1712 removed outlier: 6.442A pdb=" N TRP B1737 " --> pdb=" O LEU B1711 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 2111 through 2113 removed outlier: 6.841A pdb=" N PHE B2092 " --> pdb=" O VAL B1975 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE B1977 " --> pdb=" O PHE B2092 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N PHE B2094 " --> pdb=" O ILE B1977 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU B2095 " --> pdb=" O CYS B2054 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 2021 through 2023 removed outlier: 3.765A pdb=" N HIS B2021 " --> pdb=" O SER B2030 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU B2028 " --> pdb=" O ASP B2023 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 2075 through 2077 Processing sheet with id= AB, first strand: chain 'B' and resid 2426 through 2429 removed outlier: 7.303A pdb=" N ALA B2404 " --> pdb=" O LEU B2289 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N GLY B2291 " --> pdb=" O ALA B2404 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N MET B2406 " --> pdb=" O GLY B2291 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 2311 through 2316 removed outlier: 7.163A pdb=" N ARG B2353 " --> pdb=" O GLN B2312 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ALA B2314 " --> pdb=" O ARG B2353 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B2355 " --> pdb=" O ALA B2314 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL B2316 " --> pdb=" O VAL B2355 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TYR B2357 " --> pdb=" O VAL B2316 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 2335 through 2338 removed outlier: 3.506A pdb=" N VAL B2345 " --> pdb=" O ILE B2338 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'B' and resid 2386 through 2389 removed outlier: 3.719A pdb=" N GLU B2393 " --> pdb=" O ASP B2389 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 2804 through 2807 removed outlier: 6.484A pdb=" N ILE B2778 " --> pdb=" O LEU B2651 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU B2653 " --> pdb=" O ILE B2778 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B2780 " --> pdb=" O LEU B2653 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLY B2655 " --> pdb=" O LEU B2780 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N MET B2782 " --> pdb=" O GLY B2655 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL B2675 " --> pdb=" O VAL B2709 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU B2711 " --> pdb=" O VAL B2675 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE B2677 " --> pdb=" O LEU B2711 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 3387 through 3391 removed outlier: 6.018A pdb=" N CYS B3277 " --> pdb=" O THR B3388 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL B3390 " --> pdb=" O CYS B3277 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE B3279 " --> pdb=" O VAL B3390 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU B3368 " --> pdb=" O PRO B3278 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N LEU B3280 " --> pdb=" O LEU B3368 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU B3370 " --> pdb=" O LEU B3280 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B3301 " --> pdb=" O THR B3323 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'B' and resid 3345 through 3347 removed outlier: 3.559A pdb=" N ARG B3350 " --> pdb=" O GLN B3347 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B3355 " --> pdb=" O LYS B3358 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 3722 through 3726 Processing sheet with id= AJ, first strand: chain 'B' and resid 3752 through 3754 removed outlier: 6.235A pdb=" N CYS B3778 " --> pdb=" O VAL B3753 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'B' and resid 4198 through 4203 removed outlier: 3.929A pdb=" N VAL B4201 " --> pdb=" O GLY B4251 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B4251 " --> pdb=" O VAL B4201 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B4203 " --> pdb=" O PHE B4249 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B4249 " --> pdb=" O SER B4203 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'B' and resid 4221 through 4223 removed outlier: 3.850A pdb=" N GLU B4223 " --> pdb=" O ALA B4301 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 4226 through 4228 Processing sheet with id= AN, first strand: chain 'B' and resid 4266 through 4270 1868 hydrogen bonds defined for protein. 5400 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: 25.55 Time building geometry restraints manager: 17.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11006 1.33 - 1.45: 9190 1.45 - 1.58: 23418 1.58 - 1.70: 28 1.70 - 1.82: 300 Bond restraints: 43942 Sorted by residual: bond pdb=" C4 ATP A4402 " pdb=" C5 ATP A4402 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.35e+01 bond pdb=" C4 ATP B4402 " pdb=" C5 ATP B4402 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C5 ATP A4402 " pdb=" C6 ATP A4402 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.69e+01 bond pdb=" C5 ATP B4402 " pdb=" C6 ATP B4402 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.60e+01 bond pdb=" C5 ATP A4402 " pdb=" N7 ATP A4402 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.27e+01 ... (remaining 43937 not shown) Histogram of bond angle deviations from ideal: 98.14 - 106.83: 1402 106.83 - 115.52: 26794 115.52 - 124.21: 30425 124.21 - 132.90: 963 132.90 - 141.59: 120 Bond angle restraints: 59704 Sorted by residual: angle pdb=" PB ATP A4402 " pdb=" O3B ATP A4402 " pdb=" PG ATP A4402 " ideal model delta sigma weight residual 139.87 118.84 21.03 1.00e+00 1.00e+00 4.42e+02 angle pdb=" PB ATP B4402 " pdb=" O3B ATP B4402 " pdb=" PG ATP B4402 " ideal model delta sigma weight residual 139.87 118.84 21.03 1.00e+00 1.00e+00 4.42e+02 angle pdb=" PA ATP A4402 " pdb=" O3A ATP A4402 " pdb=" PB ATP A4402 " ideal model delta sigma weight residual 136.83 116.42 20.41 1.00e+00 1.00e+00 4.17e+02 angle pdb=" PA ATP B4402 " pdb=" O3A ATP B4402 " pdb=" PB ATP B4402 " ideal model delta sigma weight residual 136.83 116.43 20.40 1.00e+00 1.00e+00 4.16e+02 angle pdb=" C LYS A1803 " pdb=" N LEU A1804 " pdb=" CA LEU A1804 " ideal model delta sigma weight residual 120.60 135.26 -14.66 1.53e+00 4.27e-01 9.18e+01 ... (remaining 59699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.35: 26156 33.35 - 66.69: 242 66.69 - 100.04: 38 100.04 - 133.39: 6 133.39 - 166.73: 4 Dihedral angle restraints: 26446 sinusoidal: 10390 harmonic: 16056 Sorted by residual: dihedral pdb=" O2A ADP A4401 " pdb=" O3A ADP A4401 " pdb=" PA ADP A4401 " pdb=" PB ADP A4401 " ideal model delta sinusoidal sigma weight residual -60.00 106.73 -166.73 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O2A ADP B4401 " pdb=" O3A ADP B4401 " pdb=" PA ADP B4401 " pdb=" PB ADP B4401 " ideal model delta sinusoidal sigma weight residual -60.00 106.69 -166.69 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" CA SER B2462 " pdb=" C SER B2462 " pdb=" N SER B2463 " pdb=" CA SER B2463 " ideal model delta harmonic sigma weight residual -180.00 -146.89 -33.11 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 26443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5089 0.060 - 0.120: 1400 0.120 - 0.181: 238 0.181 - 0.241: 29 0.241 - 0.301: 8 Chirality restraints: 6764 Sorted by residual: chirality pdb=" CG LEU A1873 " pdb=" CB LEU A1873 " pdb=" CD1 LEU A1873 " pdb=" CD2 LEU A1873 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CG LEU B1873 " pdb=" CB LEU B1873 " pdb=" CD1 LEU B1873 " pdb=" CD2 LEU B1873 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE B1591 " pdb=" CA ILE B1591 " pdb=" CG1 ILE B1591 " pdb=" CG2 ILE B1591 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 6761 not shown) Planarity restraints: 7660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B2855 " -0.019 2.00e-02 2.50e+03 2.05e-02 7.38e+00 pdb=" CG PHE B2855 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B2855 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B2855 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B2855 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B2855 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B2855 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A2855 " 0.019 2.00e-02 2.50e+03 2.05e-02 7.37e+00 pdb=" CG PHE A2855 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A2855 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A2855 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A2855 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A2855 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A2855 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A2749 " -0.043 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A2750 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A2750 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A2750 " -0.036 5.00e-02 4.00e+02 ... (remaining 7657 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 867 2.67 - 3.23: 39942 3.23 - 3.79: 64623 3.79 - 4.34: 82759 4.34 - 4.90: 134320 Nonbonded interactions: 322511 Sorted by model distance: nonbonded pdb=" O2B ATP A4402 " pdb="MG MG A4403 " model vdw 2.116 2.170 nonbonded pdb=" O2B ATP B4402 " pdb="MG MG B4403 " model vdw 2.116 2.170 nonbonded pdb=" OE2 GLU A2095 " pdb="MG MG A4403 " model vdw 2.126 2.170 nonbonded pdb=" OE2 GLU B2095 " pdb="MG MG B4403 " model vdw 2.126 2.170 nonbonded pdb=" O SER A1752 " pdb=" OG SER A1755 " model vdw 2.253 2.440 ... (remaining 322506 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 7.000 Check model and map are aligned: 0.640 Set scattering table: 0.370 Process input model: 119.560 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.007 0.073 43942 Z= 0.469 Angle : 1.155 21.035 59704 Z= 0.676 Chirality : 0.056 0.301 6764 Planarity : 0.007 0.064 7660 Dihedral : 11.434 166.733 16034 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.35 % Allowed : 3.47 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.78 (0.09), residues: 5472 helix: -2.08 (0.07), residues: 2876 sheet: -2.05 (0.23), residues: 452 loop : -3.07 (0.11), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP B2144 HIS 0.021 0.003 HIS A1344 PHE 0.048 0.003 PHE B2855 TYR 0.027 0.003 TYR B3943 ARG 0.025 0.001 ARG A3877 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 4900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 897 time to evaluate : 5.300 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: A 1344 HIS cc_start: 0.8027 (m-70) cc_final: 0.7743 (m170) REVERT: A 1373 GLU cc_start: 0.8283 (tt0) cc_final: 0.7958 (mm-30) REVERT: A 1397 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.7951 (tt) REVERT: A 2013 MET cc_start: 0.7961 (ptp) cc_final: 0.7744 (ptp) REVERT: A 2024 MET cc_start: 0.7418 (tpt) cc_final: 0.7096 (tpp) REVERT: A 2319 SER cc_start: 0.8979 (p) cc_final: 0.8666 (m) REVERT: A 2321 GLN cc_start: 0.8140 (mm110) cc_final: 0.7714 (tp40) REVERT: A 2681 ILE cc_start: 0.8947 (mm) cc_final: 0.8710 (mt) REVERT: A 2704 GLU cc_start: 0.7542 (mp0) cc_final: 0.7337 (mt-10) REVERT: A 2815 SER cc_start: 0.8599 (m) cc_final: 0.8206 (t) REVERT: A 3195 GLU cc_start: 0.8107 (pt0) cc_final: 0.7862 (mm-30) REVERT: A 3374 ASN cc_start: 0.6815 (t0) cc_final: 0.6459 (p0) REVERT: A 3502 MET cc_start: 0.8243 (mtm) cc_final: 0.7978 (mtm) REVERT: A 3579 MET cc_start: 0.8780 (mmm) cc_final: 0.8408 (mmm) REVERT: A 3690 MET cc_start: 0.8283 (mpt) cc_final: 0.7971 (mtt) REVERT: A 3856 ASP cc_start: 0.8078 (p0) cc_final: 0.7514 (p0) REVERT: A 3918 VAL cc_start: 0.8972 (t) cc_final: 0.8764 (t) REVERT: A 4112 GLN cc_start: 0.8562 (tt0) cc_final: 0.8090 (tm-30) REVERT: B 1373 GLU cc_start: 0.8361 (tt0) cc_final: 0.7919 (mm-30) REVERT: B 1397 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.7916 (tt) REVERT: B 1817 MET cc_start: 0.8501 (mmm) cc_final: 0.8246 (mmm) REVERT: B 1943 LEU cc_start: 0.8790 (tp) cc_final: 0.7747 (tp) REVERT: B 2024 MET cc_start: 0.7273 (tpt) cc_final: 0.6983 (tpp) REVERT: B 2319 SER cc_start: 0.8960 (p) cc_final: 0.8730 (m) REVERT: B 2321 GLN cc_start: 0.8112 (mm110) cc_final: 0.7724 (tp-100) REVERT: B 2681 ILE cc_start: 0.8911 (mm) cc_final: 0.8708 (mt) REVERT: B 2815 SER cc_start: 0.8582 (m) cc_final: 0.8142 (t) REVERT: B 3374 ASN cc_start: 0.6735 (t0) cc_final: 0.6224 (p0) REVERT: B 3579 MET cc_start: 0.8747 (mmm) cc_final: 0.8506 (mmm) REVERT: B 3690 MET cc_start: 0.8267 (mpt) cc_final: 0.7927 (mtt) REVERT: B 3856 ASP cc_start: 0.8120 (p0) cc_final: 0.7509 (p0) REVERT: B 4044 LEU cc_start: 0.8933 (mt) cc_final: 0.8707 (pp) REVERT: B 4112 GLN cc_start: 0.8528 (tt0) cc_final: 0.8099 (tm-30) outliers start: 16 outliers final: 2 residues processed: 907 average time/residue: 0.6018 time to fit residues: 860.3627 Evaluate side-chains 375 residues out of total 4900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 371 time to evaluate : 4.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1440 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 464 optimal weight: 6.9990 chunk 416 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 281 optimal weight: 0.1980 chunk 222 optimal weight: 0.8980 chunk 431 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 262 optimal weight: 2.9990 chunk 320 optimal weight: 2.9990 chunk 499 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1494 ASN A1744 ASN A1905 ASN A2021 HIS A2617 HIS A2623 GLN A2624 ASN A2786 ASN ** A2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3286 GLN A3294 HIS A3327 GLN A3363 ASN A3552 GLN A3653 ASN A3773 ASN A3901 ASN A4045 ASN A4058 HIS B1310 GLN B1494 ASN B1576 ASN B1744 ASN B1810 GLN B1905 ASN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2617 HIS B2623 GLN B2624 ASN ** B2777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2786 ASN ** B2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2894 GLN B3286 GLN B3327 GLN B3363 ASN B3552 GLN B3773 ASN B4045 ASN B4058 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 43942 Z= 0.215 Angle : 0.676 11.055 59704 Z= 0.341 Chirality : 0.043 0.192 6764 Planarity : 0.005 0.051 7660 Dihedral : 8.414 172.674 6028 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.91 % Allowed : 9.60 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.96 (0.11), residues: 5472 helix: -0.35 (0.09), residues: 2864 sheet: -1.50 (0.25), residues: 434 loop : -2.53 (0.12), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B2502 HIS 0.013 0.001 HIS A2021 PHE 0.018 0.002 PHE B3392 TYR 0.025 0.002 TYR B2137 ARG 0.008 0.000 ARG A2237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 4900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 446 time to evaluate : 5.150 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: A 1278 LEU cc_start: 0.8450 (mm) cc_final: 0.8231 (mm) REVERT: A 1373 GLU cc_start: 0.8324 (tt0) cc_final: 0.7887 (mm-30) REVERT: A 1397 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8027 (pp) REVERT: A 1439 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7241 (mt-10) REVERT: A 1653 TYR cc_start: 0.7874 (m-80) cc_final: 0.7053 (m-80) REVERT: A 1907 MET cc_start: 0.8650 (mmp) cc_final: 0.8297 (mmm) REVERT: A 1988 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 2319 SER cc_start: 0.8960 (p) cc_final: 0.8604 (m) REVERT: A 2321 GLN cc_start: 0.7958 (mm110) cc_final: 0.7750 (tp-100) REVERT: A 2815 SER cc_start: 0.8533 (m) cc_final: 0.8192 (t) REVERT: A 2816 MET cc_start: 0.7215 (mtp) cc_final: 0.6761 (mtp) REVERT: A 3275 ARG cc_start: 0.7258 (mmp-170) cc_final: 0.7029 (mmp80) REVERT: A 3374 ASN cc_start: 0.6626 (t0) cc_final: 0.6034 (p0) REVERT: A 3502 MET cc_start: 0.8315 (mtm) cc_final: 0.8034 (mtm) REVERT: A 3656 MET cc_start: 0.8034 (mtp) cc_final: 0.7802 (mtp) REVERT: A 3690 MET cc_start: 0.8336 (mpt) cc_final: 0.8036 (mtt) REVERT: A 4112 GLN cc_start: 0.8423 (tt0) cc_final: 0.7834 (tm-30) REVERT: B 1351 TYR cc_start: 0.5378 (m-10) cc_final: 0.4900 (m-10) REVERT: B 1373 GLU cc_start: 0.8447 (tt0) cc_final: 0.7859 (mm-30) REVERT: B 1397 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.7642 (tt) REVERT: B 1439 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7505 (mt-10) REVERT: B 1653 TYR cc_start: 0.7897 (m-80) cc_final: 0.7102 (m-80) REVERT: B 1907 MET cc_start: 0.8580 (mmp) cc_final: 0.8347 (mmm) REVERT: B 1988 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8582 (mp) REVERT: B 2272 LEU cc_start: 0.7898 (mt) cc_final: 0.7651 (tp) REVERT: B 2319 SER cc_start: 0.8969 (p) cc_final: 0.8709 (m) REVERT: B 2321 GLN cc_start: 0.8014 (mm110) cc_final: 0.7755 (tp-100) REVERT: B 2455 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7585 (tmmt) REVERT: B 2815 SER cc_start: 0.8400 (m) cc_final: 0.8083 (t) REVERT: B 3374 ASN cc_start: 0.6628 (t0) cc_final: 0.6032 (p0) REVERT: B 3563 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7152 (mp) REVERT: B 3690 MET cc_start: 0.8343 (mpt) cc_final: 0.8017 (mtt) REVERT: B 4112 GLN cc_start: 0.8600 (tt0) cc_final: 0.8073 (tm-30) outliers start: 87 outliers final: 37 residues processed: 512 average time/residue: 0.5483 time to fit residues: 466.3417 Evaluate side-chains 375 residues out of total 4900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 332 time to evaluate : 4.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1434 ASP Chi-restraints excluded: chain A residue 1436 ASP Chi-restraints excluded: chain A residue 1747 GLU Chi-restraints excluded: chain A residue 1869 LEU Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain A residue 1988 LEU Chi-restraints excluded: chain A residue 2090 VAL Chi-restraints excluded: chain A residue 2178 HIS Chi-restraints excluded: chain A residue 2350 ASP Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3308 SER Chi-restraints excluded: chain A residue 3408 ILE Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3728 SER Chi-restraints excluded: chain A residue 4001 ASN Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4100 VAL Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1436 ASP Chi-restraints excluded: chain B residue 1747 GLU Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1869 LEU Chi-restraints excluded: chain B residue 1988 LEU Chi-restraints excluded: chain B residue 2078 MET Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2178 HIS Chi-restraints excluded: chain B residue 2350 ASP Chi-restraints excluded: chain B residue 2412 LEU Chi-restraints excluded: chain B residue 2455 LYS Chi-restraints excluded: chain B residue 2503 VAL Chi-restraints excluded: chain B residue 2556 PHE Chi-restraints excluded: chain B residue 2680 LYS Chi-restraints excluded: chain B residue 3308 SER Chi-restraints excluded: chain B residue 3408 ILE Chi-restraints excluded: chain B residue 3505 ILE Chi-restraints excluded: chain B residue 3563 LEU Chi-restraints excluded: chain B residue 3688 SER Chi-restraints excluded: chain B residue 4001 ASN Chi-restraints excluded: chain B residue 4058 HIS Chi-restraints excluded: chain B residue 4094 LEU Chi-restraints excluded: chain B residue 4116 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0405 > 50: distance: 25 - 27: 13.896 distance: 27 - 28: 17.576 distance: 28 - 29: 22.076 distance: 29 - 30: 30.407 distance: 29 - 31: 36.705 distance: 31 - 32: 14.552 distance: 32 - 33: 5.118 distance: 32 - 35: 12.257 distance: 33 - 34: 9.895 distance: 33 - 37: 12.517 distance: 35 - 36: 14.865 distance: 37 - 38: 19.632 distance: 38 - 39: 16.782 distance: 38 - 41: 10.627 distance: 39 - 40: 13.992 distance: 39 - 43: 25.194 distance: 41 - 42: 30.916 distance: 43 - 44: 6.473 distance: 44 - 45: 8.868 distance: 44 - 47: 9.174 distance: 45 - 46: 5.656 distance: 45 - 51: 4.450 distance: 47 - 48: 5.564 distance: 48 - 49: 7.791 distance: 48 - 50: 5.438 distance: 51 - 52: 12.720 distance: 52 - 53: 12.118 distance: 52 - 55: 13.596 distance: 53 - 54: 17.054 distance: 53 - 61: 13.108 distance: 55 - 56: 33.591 distance: 56 - 57: 61.040 distance: 56 - 58: 26.846 distance: 57 - 59: 53.549 distance: 58 - 60: 38.098 distance: 59 - 60: 52.115 distance: 61 - 62: 10.984 distance: 61 - 67: 7.451 distance: 62 - 63: 5.432 distance: 62 - 65: 8.976 distance: 63 - 64: 3.985 distance: 63 - 68: 4.059 distance: 65 - 66: 8.183 distance: 66 - 67: 5.709 distance: 68 - 69: 5.456 distance: 69 - 70: 9.843 distance: 69 - 72: 5.298 distance: 70 - 71: 10.568 distance: 70 - 76: 9.201 distance: 71 - 103: 7.535 distance: 72 - 73: 8.358 distance: 73 - 74: 3.371 distance: 73 - 75: 4.316 distance: 76 - 77: 17.916 distance: 77 - 78: 26.224 distance: 77 - 80: 15.723 distance: 78 - 79: 6.637 distance: 78 - 84: 21.191 distance: 80 - 81: 11.267 distance: 81 - 82: 6.520 distance: 81 - 83: 12.596 distance: 84 - 85: 18.539 distance: 85 - 86: 19.410 distance: 85 - 88: 8.292 distance: 86 - 87: 12.779 distance: 86 - 96: 20.019 distance: 88 - 89: 6.558 distance: 89 - 90: 4.037 distance: 89 - 91: 8.030 distance: 90 - 92: 3.709 distance: 91 - 93: 5.989 distance: 92 - 94: 7.056 distance: 93 - 94: 7.663 distance: 96 - 97: 9.775 distance: 97 - 98: 8.947 distance: 97 - 100: 11.084 distance: 98 - 99: 4.535 distance: 98 - 103: 4.468 distance: 99 - 124: 4.930 distance: 100 - 101: 5.360 distance: 100 - 102: 4.771