Starting phenix.real_space_refine on Wed Aug 27 00:18:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rla_4917/08_2025/6rla_4917.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rla_4917/08_2025/6rla_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 { model { file = "/net/cci-nas-00/data/ceres_data/6rla_4917/08_2025/6rla_4917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rla_4917/08_2025/6rla_4917.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rla_4917/08_2025/6rla_4917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rla_4917/08_2025/6rla_4917.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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. Time to flip 26 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43034 Number of models: 1 Model: "" Number of chains: 2 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: {'ARG:plan': 12, 'GLN:plan1': 18, 'ASP:plan': 14, 'GLU:plan': 26, 'HIS:plan': 3, 'ASN:plan1': 7, 'TYR:plan': 4, 'TRP:plan': 1} 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} Restraints were copied for chains: B Time building chain proxies: 47.45, per 1000 atoms: 1.10 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 953.7 nanoseconds 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... Secondary structure from input PDB file: 234 helices and 38 sheets defined 58.2% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 1256 through 1274 removed outlier: 3.825A pdb=" N ILE A1260 " --> pdb=" O GLY A1256 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A1272 " --> pdb=" O ASP A1268 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY A1273 " --> pdb=" O LEU A1269 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA A1274 " --> pdb=" O TRP A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1313 removed outlier: 3.956A pdb=" N ILE A1298 " --> pdb=" O ASP A1294 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A1301 " --> pdb=" O ASP A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1320 removed outlier: 6.279A pdb=" N TYR A1317 " --> pdb=" O ASP A1314 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 1321 through 1359 removed outlier: 3.644A pdb=" N VAL A1325 " --> pdb=" O PHE A1321 " (cutoff:3.500A) 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 1361 through 1385 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 1387 through 1391 removed outlier: 3.792A pdb=" N LEU A1391 " --> pdb=" O VAL A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1426 removed outlier: 4.341A pdb=" N SER A1400 " --> pdb=" O GLY A1396 " (cutoff:3.500A) 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 1431 removed outlier: 3.997A pdb=" N TYR A1430 " --> pdb=" O PRO A1427 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A1431 " --> pdb=" O ARG A1428 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1427 through 1431' Processing helix chain 'A' and resid 1433 through 1443 removed outlier: 4.050A pdb=" N GLU A1439 " --> pdb=" O ASP A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1454 Processing helix chain 'A' and resid 1496 through 1523 removed outlier: 5.006A pdb=" N ASP A1502 " --> pdb=" O THR A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1558 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 1560 through 1583 removed outlier: 3.956A pdb=" N GLU A1564 " --> pdb=" O LEU A1560 " (cutoff:3.500A) 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) removed outlier: 4.195A pdb=" N ASP A1583 " --> pdb=" O THR A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1593 through 1617 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 1623 through 1628 removed outlier: 3.648A pdb=" N LYS A1627 " --> pdb=" O ASP A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1681 removed outlier: 3.790A pdb=" N LYS A1670 " --> pdb=" O PRO A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1707 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 1720 through 1735 removed outlier: 3.602A pdb=" N ILE A1727 " --> pdb=" O SER A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1747 through 1767 removed outlier: 3.670A pdb=" N MET A1756 " --> pdb=" O SER A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1810 Processing helix chain 'A' and resid 1822 through 1833 removed outlier: 3.616A pdb=" N ALA A1826 " --> pdb=" O ASN A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1856 removed outlier: 4.563A pdb=" N ARG A1843 " --> pdb=" O LYS A1839 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A1856 " --> pdb=" O SER A1852 " (cutoff:3.500A) Processing helix chain 'A' and resid 1865 through 1886 removed outlier: 3.835A pdb=" N LEU A1869 " --> pdb=" O GLY A1865 " (cutoff:3.500A) 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 1891 through 1907 removed outlier: 4.141A pdb=" N SER A1895 " --> pdb=" O ASN A1891 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 1911 through 1926 removed outlier: 3.530A pdb=" N CYS A1915 " --> pdb=" O THR A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1937 through 1950 removed outlier: 3.679A pdb=" N ALA A1942 " --> pdb=" O GLU A1938 " (cutoff:3.500A) Processing helix chain 'A' and resid 1955 through 1972 Processing helix chain 'A' and resid 1986 through 1998 removed outlier: 4.251A pdb=" N ALA A1994 " --> pdb=" O ARG A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2019 Processing helix chain 'A' and resid 2032 through 2044 removed outlier: 3.845A pdb=" N GLU A2044 " --> pdb=" O GLN A2040 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2064 Processing helix chain 'A' and resid 2065 through 2067 No H-bonds generated for 'chain 'A' and resid 2065 through 2067' Processing helix chain 'A' and resid 2103 through 2108 removed outlier: 3.506A pdb=" N ILE A2107 " --> pdb=" O SER A2103 " (cutoff:3.500A) Processing helix chain 'A' and resid 2122 through 2132 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 2137 through 2160 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 2167 through 2177 Processing helix chain 'A' and resid 2184 through 2197 removed outlier: 3.712A pdb=" N ILE A2190 " --> pdb=" O ASP A2186 " (cutoff:3.500A) Processing helix chain 'A' and resid 2201 through 2215 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 2265 through 2276 Processing helix chain 'A' and resid 2296 through 2307 removed outlier: 3.607A pdb=" N LEU A2300 " --> pdb=" O GLY A2296 " (cutoff:3.500A) Processing helix chain 'A' and resid 2323 through 2333 removed outlier: 3.944A pdb=" N LEU A2327 " --> pdb=" O THR A2323 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2385 Processing helix chain 'A' and resid 2418 through 2425 removed outlier: 3.765A pdb=" N ILE A2424 " --> pdb=" O ARG A2420 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A2425 " --> pdb=" O PHE A2421 " (cutoff:3.500A) Processing helix chain 'A' and resid 2434 through 2451 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 2463 through 2484 Processing helix chain 'A' and resid 2495 through 2504 removed outlier: 4.213A pdb=" N LEU A2499 " --> pdb=" O THR A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2508 Processing helix chain 'A' and resid 2519 through 2536 removed outlier: 3.740A pdb=" N VAL A2523 " --> pdb=" O PRO A2519 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A2526 " --> pdb=" O TYR A2522 " (cutoff:3.500A) Processing helix chain 'A' and resid 2537 through 2539 No H-bonds generated for 'chain 'A' and resid 2537 through 2539' Processing helix chain 'A' and resid 2541 through 2560 Processing helix chain 'A' and resid 2603 through 2621 removed outlier: 4.141A pdb=" N ASP A2621 " --> pdb=" O HIS A2617 " (cutoff:3.500A) Processing helix chain 'A' and resid 2630 through 2645 removed outlier: 3.662A pdb=" N VAL A2643 " --> pdb=" O ARG A2639 " (cutoff:3.500A) Processing helix chain 'A' and resid 2661 through 2672 Processing helix chain 'A' and resid 2687 through 2704 Processing helix chain 'A' and resid 2715 through 2717 No H-bonds generated for 'chain 'A' and resid 2715 through 2717' Processing helix chain 'A' and resid 2721 through 2732 Processing helix chain 'A' and resid 2744 through 2749 Processing helix chain 'A' and resid 2751 through 2759 removed outlier: 3.651A pdb=" N GLY A2759 " --> pdb=" O ALA A2755 " (cutoff:3.500A) Processing helix chain 'A' and resid 2763 through 2775 removed outlier: 4.217A pdb=" N TYR A2767 " --> pdb=" O PRO A2763 " (cutoff:3.500A) Processing helix chain 'A' and resid 2786 through 2789 removed outlier: 3.681A pdb=" N PHE A2789 " --> pdb=" O ASN A2786 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2786 through 2789' Processing helix chain 'A' and resid 2790 through 2795 Processing helix chain 'A' and resid 2796 through 2801 Processing helix chain 'A' and resid 2812 through 2823 removed outlier: 3.787A pdb=" N MET A2816 " --> pdb=" O SER A2812 " (cutoff:3.500A) 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 2863 removed outlier: 3.621A pdb=" N LEU A2852 " --> pdb=" O ASP A2848 " (cutoff:3.500A) Processing helix chain 'A' and resid 2864 through 2866 No H-bonds generated for 'chain 'A' and resid 2864 through 2866' Processing helix chain 'A' and resid 2868 through 2912 removed outlier: 3.584A pdb=" N ASN A2905 " --> pdb=" O VAL A2901 " (cutoff:3.500A) Processing helix chain 'A' and resid 2913 through 2925 Processing helix chain 'A' and resid 3168 through 3187 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 3188 through 3197 Processing helix chain 'A' and resid 3199 through 3214 removed outlier: 4.083A pdb=" N ARG A3203 " --> pdb=" O THR A3199 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A3211 " --> pdb=" O ALA A3207 " (cutoff:3.500A) Processing helix chain 'A' and resid 3218 through 3234 Processing helix chain 'A' and resid 3240 through 3245 Processing helix chain 'A' and resid 3246 through 3255 Processing helix chain 'A' and resid 3261 through 3271 removed outlier: 3.501A pdb=" N ILE A3271 " --> pdb=" O ASN A3267 " (cutoff:3.500A) Processing helix chain 'A' and resid 3285 through 3295 Processing helix chain 'A' and resid 3309 through 3320 Processing helix chain 'A' and resid 3336 through 3341 Processing helix chain 'A' and resid 3395 through 3412 removed outlier: 3.596A pdb=" N GLY A3401 " --> pdb=" O SER A3397 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A3412 " --> pdb=" O ILE A3408 " (cutoff:3.500A) Processing helix chain 'A' and resid 3412 through 3437 removed outlier: 3.732A pdb=" N GLU A3416 " --> pdb=" O LYS A3412 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A3423 " --> pdb=" O LYS A3419 " (cutoff:3.500A) Processing helix chain 'A' and resid 3439 through 3446 Processing helix chain 'A' and resid 3455 through 3490 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 3492 through 3508 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) Processing helix chain 'A' and resid 3520 through 3533 removed outlier: 3.869A pdb=" N LEU A3531 " --> pdb=" O PHE A3527 " (cutoff:3.500A) Processing helix chain 'A' and resid 3540 through 3561 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 3567 through 3580 Processing helix chain 'A' and resid 3588 through 3593 Processing helix chain 'A' and resid 3619 through 3633 removed outlier: 4.209A pdb=" N ALA A3625 " --> pdb=" O GLU A3621 " (cutoff:3.500A) Processing helix chain 'A' and resid 3633 through 3641 removed outlier: 3.638A pdb=" N TYR A3637 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS A3641 " --> pdb=" O TYR A3637 " (cutoff:3.500A) Processing helix chain 'A' and resid 3646 through 3652 removed outlier: 3.704A pdb=" N THR A3650 " --> pdb=" O ALA A3646 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3666 Processing helix chain 'A' and resid 3670 through 3682 removed outlier: 3.773A pdb=" N ILE A3675 " --> pdb=" O LEU A3671 " (cutoff:3.500A) Processing helix chain 'A' and resid 3685 through 3699 Processing helix chain 'A' and resid 3733 through 3745 Processing helix chain 'A' and resid 3759 through 3774 removed outlier: 3.891A pdb=" N GLN A3765 " --> pdb=" O ASP A3761 " (cutoff:3.500A) Processing helix chain 'A' and resid 3788 through 3799 Processing helix chain 'A' and resid 3818 through 3824 removed outlier: 3.908A pdb=" N LEU A3822 " --> pdb=" O THR A3818 " (cutoff:3.500A) Processing helix chain 'A' and resid 3835 through 3847 Processing helix chain 'A' and resid 3848 through 3853 removed outlier: 3.695A pdb=" N ILE A3852 " --> pdb=" O THR A3848 " (cutoff:3.500A) Processing helix chain 'A' and resid 3857 through 3877 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) Processing helix chain 'A' and resid 3878 through 3880 No H-bonds generated for 'chain 'A' and resid 3878 through 3880' Processing helix chain 'A' and resid 3892 through 3908 removed outlier: 3.586A pdb=" N LEU A3896 " --> pdb=" O SER A3892 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3926 removed outlier: 3.757A pdb=" N VAL A3918 " --> pdb=" O GLN A3914 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS A3919 " --> pdb=" O TRP A3915 " (cutoff:3.500A) Processing helix chain 'A' and resid 3927 through 3931 Processing helix chain 'A' and resid 3933 through 3947 removed outlier: 3.725A pdb=" N LEU A3937 " --> pdb=" O ASN A3933 " (cutoff:3.500A) Processing helix chain 'A' and resid 3976 through 3987 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 4000 through 4021 removed outlier: 3.802A pdb=" N ARG A4004 " --> pdb=" O ALA A4000 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A4021 " --> pdb=" O GLN A4017 " (cutoff:3.500A) Processing helix chain 'A' and resid 4033 through 4037 Processing helix chain 'A' and resid 4040 through 4051 removed outlier: 3.901A pdb=" N LEU A4044 " --> pdb=" O LEU A4040 " (cutoff:3.500A) Processing helix chain 'A' and resid 4072 through 4100 removed outlier: 3.613A pdb=" N ILE A4076 " --> pdb=" O ILE A4072 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A4097 " --> pdb=" O SER A4093 " (cutoff:3.500A) Processing helix chain 'A' and resid 4109 through 4120 Processing helix chain 'A' and resid 4124 through 4131 removed outlier: 3.845A pdb=" N LYS A4130 " --> pdb=" O ALA A4126 " (cutoff:3.500A) Processing helix chain 'A' and resid 4136 through 4159 removed outlier: 4.049A pdb=" N GLN A4152 " --> pdb=" O ALA A4148 " (cutoff:3.500A) Processing helix chain 'A' and resid 4171 through 4173 No H-bonds generated for 'chain 'A' and resid 4171 through 4173' Processing helix chain 'A' and resid 4175 through 4192 removed outlier: 3.567A pdb=" N PHE A4179 " --> pdb=" O HIS A4175 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A4192 " --> pdb=" O ALA A4188 " (cutoff:3.500A) Processing helix chain 'A' and resid 4194 through 4196 No H-bonds generated for 'chain 'A' and resid 4194 through 4196' Processing helix chain 'A' and resid 4262 through 4264 No H-bonds generated for 'chain 'A' and resid 4262 through 4264' Processing helix chain 'A' and resid 4292 through 4298 Processing helix chain 'B' and resid 1256 through 1274 removed outlier: 3.825A pdb=" N ILE B1260 " --> pdb=" O GLY B1256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B1272 " --> pdb=" O ASP B1268 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY B1273 " --> pdb=" O LEU B1269 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B1274 " --> pdb=" O TRP B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1294 through 1313 removed outlier: 3.957A pdb=" N ILE B1298 " --> pdb=" O ASP B1294 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B1301 " --> pdb=" O ASP B1297 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1320 removed outlier: 6.278A pdb=" N TYR B1317 " --> pdb=" O ASP B1314 " (cutoff:3.500A) 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) Processing helix chain 'B' and resid 1321 through 1359 removed outlier: 3.644A pdb=" N VAL B1325 " --> pdb=" O PHE B1321 " (cutoff:3.500A) 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 1361 through 1385 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 1387 through 1391 removed outlier: 3.793A pdb=" N LEU B1391 " --> pdb=" O VAL B1388 " (cutoff:3.500A) Processing helix chain 'B' and resid 1396 through 1426 removed outlier: 4.341A pdb=" N SER B1400 " --> pdb=" O GLY B1396 " (cutoff:3.500A) 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 1431 removed outlier: 3.996A pdb=" N TYR B1430 " --> pdb=" O PRO B1427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B1431 " --> pdb=" O ARG B1428 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1427 through 1431' Processing helix chain 'B' and resid 1433 through 1443 removed outlier: 4.049A pdb=" N GLU B1439 " --> pdb=" O ASP B1435 " (cutoff:3.500A) Processing helix chain 'B' and resid 1446 through 1454 Processing helix chain 'B' and resid 1496 through 1523 removed outlier: 5.006A pdb=" N ASP B1502 " --> pdb=" O THR B1498 " (cutoff:3.500A) Processing helix chain 'B' and resid 1535 through 1558 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 1560 through 1583 removed outlier: 3.955A pdb=" N GLU B1564 " --> pdb=" O LEU B1560 " (cutoff:3.500A) 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) removed outlier: 4.195A pdb=" N ASP B1583 " --> pdb=" O THR B1579 " (cutoff:3.500A) Processing helix chain 'B' and resid 1593 through 1617 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 1623 through 1628 removed outlier: 3.648A pdb=" N LYS B1627 " --> pdb=" O ASP B1623 " (cutoff:3.500A) Processing helix chain 'B' and resid 1666 through 1681 removed outlier: 3.789A pdb=" N LYS B1670 " --> pdb=" O PRO B1666 " (cutoff:3.500A) Processing helix chain 'B' and resid 1694 through 1707 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 1720 through 1735 removed outlier: 3.602A pdb=" N ILE B1727 " --> pdb=" O SER B1723 " (cutoff:3.500A) Processing helix chain 'B' and resid 1747 through 1767 removed outlier: 3.671A pdb=" N MET B1756 " --> pdb=" O SER B1752 " (cutoff:3.500A) Processing helix chain 'B' and resid 1805 through 1810 Processing helix chain 'B' and resid 1822 through 1833 removed outlier: 3.617A pdb=" N ALA B1826 " --> pdb=" O ASN B1822 " (cutoff:3.500A) Processing helix chain 'B' and resid 1837 through 1856 removed outlier: 4.562A pdb=" N ARG B1843 " --> pdb=" O LYS B1839 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B1856 " --> pdb=" O SER B1852 " (cutoff:3.500A) Processing helix chain 'B' and resid 1865 through 1886 removed outlier: 3.835A pdb=" N LEU B1869 " --> pdb=" O GLY B1865 " (cutoff:3.500A) 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 1891 through 1907 removed outlier: 4.140A pdb=" N SER B1895 " --> pdb=" O ASN B1891 " (cutoff:3.500A) 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) Processing helix chain 'B' and resid 1911 through 1926 removed outlier: 3.530A pdb=" N CYS B1915 " --> pdb=" O THR B1911 " (cutoff:3.500A) Processing helix chain 'B' and resid 1937 through 1950 removed outlier: 3.679A pdb=" N ALA B1942 " --> pdb=" O GLU B1938 " (cutoff:3.500A) Processing helix chain 'B' and resid 1955 through 1972 Processing helix chain 'B' and resid 1986 through 1998 removed outlier: 4.251A pdb=" N ALA B1994 " --> pdb=" O ARG B1990 " (cutoff:3.500A) Processing helix chain 'B' and resid 2014 through 2019 Processing helix chain 'B' and resid 2032 through 2044 removed outlier: 3.845A pdb=" N GLU B2044 " --> pdb=" O GLN B2040 " (cutoff:3.500A) Processing helix chain 'B' and resid 2059 through 2064 Processing helix chain 'B' and resid 2065 through 2067 No H-bonds generated for 'chain 'B' and resid 2065 through 2067' Processing helix chain 'B' and resid 2103 through 2108 removed outlier: 3.507A pdb=" N ILE B2107 " --> pdb=" O SER B2103 " (cutoff:3.500A) Processing helix chain 'B' and resid 2122 through 2132 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 2137 through 2160 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 2167 through 2177 Processing helix chain 'B' and resid 2184 through 2197 removed outlier: 3.712A pdb=" N ILE B2190 " --> pdb=" O ASP B2186 " (cutoff:3.500A) Processing helix chain 'B' and resid 2201 through 2215 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 2265 through 2276 Processing helix chain 'B' and resid 2296 through 2307 removed outlier: 3.607A pdb=" N LEU B2300 " --> pdb=" O GLY B2296 " (cutoff:3.500A) Processing helix chain 'B' and resid 2323 through 2333 removed outlier: 3.945A pdb=" N LEU B2327 " --> pdb=" O THR B2323 " (cutoff:3.500A) Processing helix chain 'B' and resid 2372 through 2385 Processing helix chain 'B' and resid 2418 through 2425 removed outlier: 3.765A pdb=" N ILE B2424 " --> pdb=" O ARG B2420 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL B2425 " --> pdb=" O PHE B2421 " (cutoff:3.500A) Processing helix chain 'B' and resid 2434 through 2451 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 2463 through 2484 Processing helix chain 'B' and resid 2495 through 2504 removed outlier: 4.213A pdb=" N LEU B2499 " --> pdb=" O THR B2495 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2508 Processing helix chain 'B' and resid 2519 through 2536 removed outlier: 3.741A pdb=" N VAL B2523 " --> pdb=" O PRO B2519 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B2526 " --> pdb=" O TYR B2522 " (cutoff:3.500A) Processing helix chain 'B' and resid 2537 through 2539 No H-bonds generated for 'chain 'B' and resid 2537 through 2539' Processing helix chain 'B' and resid 2541 through 2560 Processing helix chain 'B' and resid 2603 through 2621 removed outlier: 4.142A pdb=" N ASP B2621 " --> pdb=" O HIS B2617 " (cutoff:3.500A) Processing helix chain 'B' and resid 2630 through 2645 removed outlier: 3.662A pdb=" N VAL B2643 " --> pdb=" O ARG B2639 " (cutoff:3.500A) Processing helix chain 'B' and resid 2661 through 2672 Processing helix chain 'B' and resid 2687 through 2704 Processing helix chain 'B' and resid 2715 through 2717 No H-bonds generated for 'chain 'B' and resid 2715 through 2717' Processing helix chain 'B' and resid 2721 through 2732 Processing helix chain 'B' and resid 2744 through 2749 Processing helix chain 'B' and resid 2751 through 2759 removed outlier: 3.651A pdb=" N GLY B2759 " --> pdb=" O ALA B2755 " (cutoff:3.500A) Processing helix chain 'B' and resid 2763 through 2775 removed outlier: 4.217A pdb=" N TYR B2767 " --> pdb=" O PRO B2763 " (cutoff:3.500A) Processing helix chain 'B' and resid 2786 through 2789 removed outlier: 3.681A pdb=" N PHE B2789 " --> pdb=" O ASN B2786 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2786 through 2789' Processing helix chain 'B' and resid 2790 through 2795 Processing helix chain 'B' and resid 2796 through 2801 Processing helix chain 'B' and resid 2812 through 2823 removed outlier: 3.787A pdb=" N MET B2816 " --> pdb=" O SER B2812 " (cutoff:3.500A) 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 2863 removed outlier: 3.621A pdb=" N LEU B2852 " --> pdb=" O ASP B2848 " (cutoff:3.500A) Processing helix chain 'B' and resid 2864 through 2866 No H-bonds generated for 'chain 'B' and resid 2864 through 2866' Processing helix chain 'B' and resid 2868 through 2912 removed outlier: 3.584A pdb=" N ASN B2905 " --> pdb=" O VAL B2901 " (cutoff:3.500A) Processing helix chain 'B' and resid 2913 through 2925 Processing helix chain 'B' and resid 3168 through 3187 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 3188 through 3197 Processing helix chain 'B' and resid 3199 through 3214 removed outlier: 4.083A pdb=" N ARG B3203 " --> pdb=" O THR B3199 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B3211 " --> pdb=" O ALA B3207 " (cutoff:3.500A) Processing helix chain 'B' and resid 3218 through 3234 Processing helix chain 'B' and resid 3240 through 3245 Processing helix chain 'B' and resid 3246 through 3255 Processing helix chain 'B' and resid 3261 through 3271 removed outlier: 3.501A pdb=" N ILE B3271 " --> pdb=" O ASN B3267 " (cutoff:3.500A) Processing helix chain 'B' and resid 3285 through 3295 Processing helix chain 'B' and resid 3309 through 3320 Processing helix chain 'B' and resid 3336 through 3341 Processing helix chain 'B' and resid 3395 through 3412 removed outlier: 3.597A pdb=" N GLY B3401 " --> pdb=" O SER B3397 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B3412 " --> pdb=" O ILE B3408 " (cutoff:3.500A) Processing helix chain 'B' and resid 3412 through 3437 removed outlier: 3.732A pdb=" N GLU B3416 " --> pdb=" O LYS B3412 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B3423 " --> pdb=" O LYS B3419 " (cutoff:3.500A) Processing helix chain 'B' and resid 3439 through 3446 Processing helix chain 'B' and resid 3455 through 3490 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 3492 through 3508 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) Processing helix chain 'B' and resid 3520 through 3533 removed outlier: 3.869A pdb=" N LEU B3531 " --> pdb=" O PHE B3527 " (cutoff:3.500A) Processing helix chain 'B' and resid 3540 through 3561 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 3567 through 3580 Processing helix chain 'B' and resid 3588 through 3593 Processing helix chain 'B' and resid 3619 through 3633 removed outlier: 4.210A pdb=" N ALA B3625 " --> pdb=" O GLU B3621 " (cutoff:3.500A) Processing helix chain 'B' and resid 3633 through 3641 removed outlier: 3.638A pdb=" N TYR B3637 " --> pdb=" O LEU B3633 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS B3641 " --> pdb=" O TYR B3637 " (cutoff:3.500A) Processing helix chain 'B' and resid 3646 through 3652 removed outlier: 3.703A pdb=" N THR B3650 " --> pdb=" O ALA B3646 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3666 Processing helix chain 'B' and resid 3670 through 3682 removed outlier: 3.772A pdb=" N ILE B3675 " --> pdb=" O LEU B3671 " (cutoff:3.500A) Processing helix chain 'B' and resid 3685 through 3699 Processing helix chain 'B' and resid 3733 through 3745 Processing helix chain 'B' and resid 3759 through 3774 removed outlier: 3.892A pdb=" N GLN B3765 " --> pdb=" O ASP B3761 " (cutoff:3.500A) Processing helix chain 'B' and resid 3788 through 3799 Processing helix chain 'B' and resid 3818 through 3824 removed outlier: 3.908A pdb=" N LEU B3822 " --> pdb=" O THR B3818 " (cutoff:3.500A) Processing helix chain 'B' and resid 3835 through 3847 Processing helix chain 'B' and resid 3848 through 3853 removed outlier: 3.695A pdb=" N ILE B3852 " --> pdb=" O THR B3848 " (cutoff:3.500A) Processing helix chain 'B' and resid 3857 through 3877 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) Processing helix chain 'B' and resid 3878 through 3880 No H-bonds generated for 'chain 'B' and resid 3878 through 3880' Processing helix chain 'B' and resid 3892 through 3908 removed outlier: 3.585A pdb=" N LEU B3896 " --> pdb=" O SER B3892 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3926 removed outlier: 3.758A pdb=" N VAL B3918 " --> pdb=" O GLN B3914 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS B3919 " --> pdb=" O TRP B3915 " (cutoff:3.500A) Processing helix chain 'B' and resid 3927 through 3931 Processing helix chain 'B' and resid 3933 through 3947 removed outlier: 3.725A pdb=" N LEU B3937 " --> pdb=" O ASN B3933 " (cutoff:3.500A) Processing helix chain 'B' and resid 3976 through 3987 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 4000 through 4021 removed outlier: 3.803A pdb=" N ARG B4004 " --> pdb=" O ALA B4000 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B4021 " --> pdb=" O GLN B4017 " (cutoff:3.500A) Processing helix chain 'B' and resid 4033 through 4037 Processing helix chain 'B' and resid 4040 through 4051 removed outlier: 3.902A pdb=" N LEU B4044 " --> pdb=" O LEU B4040 " (cutoff:3.500A) Processing helix chain 'B' and resid 4072 through 4100 removed outlier: 3.613A pdb=" N ILE B4076 " --> pdb=" O ILE B4072 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B4097 " --> pdb=" O SER B4093 " (cutoff:3.500A) Processing helix chain 'B' and resid 4109 through 4120 Processing helix chain 'B' and resid 4124 through 4131 removed outlier: 3.846A pdb=" N LYS B4130 " --> pdb=" O ALA B4126 " (cutoff:3.500A) Processing helix chain 'B' and resid 4136 through 4159 removed outlier: 4.049A pdb=" N GLN B4152 " --> pdb=" O ALA B4148 " (cutoff:3.500A) Processing helix chain 'B' and resid 4171 through 4173 No H-bonds generated for 'chain 'B' and resid 4171 through 4173' Processing helix chain 'B' and resid 4175 through 4192 removed outlier: 3.567A pdb=" N PHE B4179 " --> pdb=" O HIS B4175 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B4192 " --> pdb=" O ALA B4188 " (cutoff:3.500A) Processing helix chain 'B' and resid 4194 through 4196 No H-bonds generated for 'chain 'B' and resid 4194 through 4196' Processing helix chain 'B' and resid 4262 through 4264 No H-bonds generated for 'chain 'B' and resid 4262 through 4264' Processing helix chain 'B' and resid 4292 through 4298 Processing sheet with id=AA1, first strand: chain 'A' and resid 1278 through 1281 Processing sheet with id=AA2, first strand: chain 'A' and resid 1472 through 1476 removed outlier: 9.217A pdb=" N HIS A1472 " --> pdb=" O ASN A1488 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N ASN A1488 " --> pdb=" O HIS A1472 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR A1474 " --> pdb=" O PHE A1486 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, first strand: chain 'A' and resid 1686 through 1688 Processing sheet with id=AA5, first strand: chain 'A' and resid 1710 through 1712 removed outlier: 3.825A pdb=" N CYS A1739 " --> pdb=" O LEU A1711 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY A1738 " --> pdb=" O PHE A1788 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR A1790 " --> pdb=" O GLY A1738 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE A1740 " --> pdb=" O THR A1790 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2004 through 2008 removed outlier: 6.727A pdb=" N LYS A2004 " --> pdb=" O TRP A2051 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A2053 " --> pdb=" O LYS A2004 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR A2006 " --> pdb=" O ILE A2053 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER A2050 " --> pdb=" O ASN A2091 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL A2093 " --> pdb=" O SER A2050 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A2052 " --> pdb=" O VAL A2093 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLU A2095 " --> pdb=" O ILE A2052 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS A2054 " --> pdb=" O GLU A2095 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A1975 " --> pdb=" O PHE A2094 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLY A1974 " --> pdb=" O GLY A2111 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE A2113 " --> pdb=" O GLY A1974 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL A1976 " --> pdb=" O ILE A2113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, 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=AA8, first strand: chain 'A' and resid 2075 through 2077 Processing sheet with id=AA9, first strand: chain 'A' and resid 2404 through 2407 removed outlier: 3.629A pdb=" N LEU A2289 " --> pdb=" O ALA A2404 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET A2406 " --> pdb=" O LEU A2289 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A2291 " --> pdb=" O MET A2406 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A2288 " --> pdb=" O CYS A2428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2311 through 2316 removed outlier: 3.577A pdb=" N GLN A2312 " --> pdb=" O ARG A2353 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU A2354 " --> pdb=" O GLN A2401 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2335 through 2338 removed outlier: 3.506A pdb=" N VAL A2345 " --> pdb=" O ILE A2338 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A2393 " --> pdb=" O ASP A2389 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2675 through 2677 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) removed outlier: 7.988A pdb=" N GLU A2713 " --> pdb=" O PHE A2677 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A2655 " --> pdb=" O MET A2782 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3300 through 3303 removed outlier: 6.501A pdb=" N GLU A3301 " --> pdb=" O ILE A3325 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLN A3327 " --> pdb=" O GLU A3301 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ILE A3303 " --> pdb=" O GLN A3327 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N MET A3329 " --> pdb=" O ILE A3303 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU A3324 " --> pdb=" O PHE A3369 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER A3371 " --> pdb=" O LEU A3324 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A3326 " --> pdb=" O SER A3371 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU A3370 " --> pdb=" O PRO A3278 " (cutoff:3.500A) 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) Processing sheet with id=AB5, 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=AB6, first strand: chain 'A' and resid 3752 through 3754 removed outlier: 6.254A pdb=" N LEU A3777 " --> pdb=" O TRP A3808 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N THR A3810 " --> pdb=" O LEU A3777 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU A3779 " --> pdb=" O THR A3810 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A3723 " --> pdb=" O LEU A3809 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA A3811 " --> pdb=" O ILE A3723 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE A3725 " --> pdb=" O ALA A3811 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4168 through 4169 removed outlier: 3.763A pdb=" N SER A4218 " --> pdb=" O LEU A4168 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A4249 " --> pdb=" O SER A4203 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A4203 " --> pdb=" O PHE A4249 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A4251 " --> pdb=" O VAL A4201 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A4201 " --> pdb=" O GLY A4251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4243 through 4244 removed outlier: 3.850A pdb=" N GLU A4223 " --> pdb=" O ALA A4301 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4226 through 4228 Processing sheet with id=AC1, first strand: chain 'A' and resid 4266 through 4270 Processing sheet with id=AC2, first strand: chain 'B' and resid 1278 through 1281 Processing sheet with id=AC3, first strand: chain 'B' and resid 1472 through 1476 removed outlier: 9.218A pdb=" N HIS B1472 " --> pdb=" O ASN B1488 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N ASN B1488 " --> pdb=" O HIS B1472 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR B1474 " --> pdb=" O PHE B1486 " (cutoff:3.500A) Processing sheet with id=AC4, 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=AC5, first strand: chain 'B' and resid 1686 through 1688 Processing sheet with id=AC6, first strand: chain 'B' and resid 1710 through 1712 removed outlier: 3.825A pdb=" N CYS B1739 " --> pdb=" O LEU B1711 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLY B1738 " --> pdb=" O PHE B1788 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR B1790 " --> pdb=" O GLY B1738 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE B1740 " --> pdb=" O THR B1790 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 2004 through 2008 removed outlier: 6.727A pdb=" N LYS B2004 " --> pdb=" O TRP B2051 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE B2053 " --> pdb=" O LYS B2004 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR B2006 " --> pdb=" O ILE B2053 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER B2050 " --> pdb=" O ASN B2091 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL B2093 " --> pdb=" O SER B2050 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B2052 " --> pdb=" O VAL B2093 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLU B2095 " --> pdb=" O ILE B2052 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS B2054 " --> pdb=" O GLU B2095 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B1975 " --> pdb=" O PHE B2094 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLY B1974 " --> pdb=" O GLY B2111 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE B2113 " --> pdb=" O GLY B1974 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL B1976 " --> pdb=" O ILE B2113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, 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=AC9, first strand: chain 'B' and resid 2075 through 2077 Processing sheet with id=AD1, first strand: chain 'B' and resid 2404 through 2407 removed outlier: 3.629A pdb=" N LEU B2289 " --> pdb=" O ALA B2404 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B2406 " --> pdb=" O LEU B2289 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY B2291 " --> pdb=" O MET B2406 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE B2288 " --> pdb=" O CYS B2428 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 2311 through 2316 removed outlier: 3.578A pdb=" N GLN B2312 " --> pdb=" O ARG B2353 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU B2354 " --> pdb=" O GLN B2401 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 2335 through 2338 removed outlier: 3.506A pdb=" N VAL B2345 " --> pdb=" O ILE B2338 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B2393 " --> pdb=" O ASP B2389 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 2675 through 2677 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) removed outlier: 7.989A pdb=" N GLU B2713 " --> pdb=" O PHE B2677 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B2655 " --> pdb=" O MET B2782 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 3300 through 3303 removed outlier: 6.500A pdb=" N GLU B3301 " --> pdb=" O ILE B3325 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLN B3327 " --> pdb=" O GLU B3301 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ILE B3303 " --> pdb=" O GLN B3327 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET B3329 " --> pdb=" O ILE B3303 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU B3324 " --> pdb=" O PHE B3369 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N SER B3371 " --> pdb=" O LEU B3324 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B3326 " --> pdb=" O SER B3371 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU B3370 " --> pdb=" O PRO B3278 " (cutoff:3.500A) 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) Processing sheet with id=AD6, 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=AD7, first strand: chain 'B' and resid 3752 through 3754 removed outlier: 6.253A pdb=" N LEU B3777 " --> pdb=" O TRP B3808 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N THR B3810 " --> pdb=" O LEU B3777 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU B3779 " --> pdb=" O THR B3810 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE B3723 " --> pdb=" O LEU B3809 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA B3811 " --> pdb=" O ILE B3723 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE B3725 " --> pdb=" O ALA B3811 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 4168 through 4169 removed outlier: 3.761A pdb=" N SER B4218 " --> pdb=" O LEU B4168 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B4249 " --> pdb=" O SER B4203 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B4203 " --> pdb=" O PHE B4249 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B4251 " --> pdb=" O VAL B4201 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B4201 " --> pdb=" O GLY B4251 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 4243 through 4244 removed outlier: 3.850A pdb=" N GLU B4223 " --> pdb=" O ALA B4301 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 4226 through 4228 Processing sheet with id=AE2, first strand: chain 'B' and resid 4266 through 4270 2156 hydrogen bonds defined for protein. 6318 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: 14.66 Time building geometry restraints manager: 4.99 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: 0.00 - 4.21: 59146 4.21 - 8.41: 520 8.41 - 12.62: 24 12.62 - 16.83: 10 16.83 - 21.03: 4 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: 863 2.67 - 3.23: 39706 3.23 - 3.79: 64405 3.79 - 4.34: 82150 4.34 - 4.90: 134235 Nonbonded interactions: 321359 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 3.040 ... (remaining 321354 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 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: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 84.320 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.910 ------------------------------------------------------------------------------- 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 43944 Z= 0.341 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 : 3.81 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.025 0.001 ARG A3877 TYR 0.027 0.003 TYR B3943 PHE 0.048 0.003 PHE B2855 TRP 0.030 0.004 TRP B2144 HIS 0.021 0.003 HIS A1344 Details of bonding type rmsd covalent geometry : bond 0.00718 (43942) covalent geometry : angle 1.15529 (59704) hydrogen bonds : bond 0.16034 ( 2156) hydrogen bonds : angle 6.35175 ( 6318) Misc. bond : bond 0.00182 ( 2) *********************** 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 to be fit. rotamer outliers: 16 poor density : 897 time to evaluate : 1.747 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: 0.7744 (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: 0.7950 (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: 0.7097 (tpp) REVERT: A 2319 SER cc_start: 0.8979 (p) cc_final: 0.8667 (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: 0.7977 (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: 0.7970 (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: 0.8766 (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: 0.7915 (tt) REVERT: B 1817 MET cc_start: 0.8501 (mmm) cc_final: 0.8255 (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: 0.8731 (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: 0.8098 (tm-30) outliers start: 16 outliers final: 2 residues processed: 907 average time/residue: 0.2953 time to fit residues: 424.1108 Evaluate side-chains 376 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 372 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 394 optimal weight: 6.9990 chunk 430 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 A2777 HIS A2786 ASN ** A2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3286 GLN A3294 HIS A3363 ASN ** A3552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3901 ASN B1310 GLN B1494 ASN B1744 ASN B1792 ASN B1810 GLN B1905 ASN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2617 HIS B2623 GLN B2777 HIS B2786 ASN ** B2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3286 GLN B3294 HIS B3363 ASN ** B3552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4045 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.096774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.082512 restraints weight = 138933.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.084242 restraints weight = 83388.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.085428 restraints weight = 58445.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.086222 restraints weight = 45468.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.086663 restraints weight = 38186.758| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 43944 Z= 0.141 Angle : 0.684 11.071 59704 Z= 0.347 Chirality : 0.043 0.181 6764 Planarity : 0.005 0.048 7660 Dihedral : 8.322 167.765 6028 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.67 % Allowed : 9.21 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.11), residues: 5472 helix: -0.36 (0.09), residues: 2960 sheet: -1.50 (0.24), residues: 476 loop : -2.66 (0.12), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2237 TYR 0.023 0.002 TYR B2137 PHE 0.020 0.001 PHE A3238 TRP 0.031 0.002 TRP B2502 HIS 0.012 0.001 HIS A2021 Details of bonding type rmsd covalent geometry : bond 0.00306 (43942) covalent geometry : angle 0.68432 (59704) hydrogen bonds : bond 0.04946 ( 2156) hydrogen bonds : angle 4.58679 ( 6318) Misc. bond : bond 0.00075 ( 2) *********************** 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 571 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 495 time to evaluate : 1.611 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: A 1278 LEU cc_start: 0.8307 (mm) cc_final: 0.8069 (mm) REVERT: A 1373 GLU cc_start: 0.8253 (tt0) cc_final: 0.7892 (mm-30) REVERT: A 1397 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7636 (tt) REVERT: A 1907 MET cc_start: 0.8605 (mmp) cc_final: 0.8172 (mmm) REVERT: A 1988 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8522 (mp) REVERT: A 2319 SER cc_start: 0.9008 (p) cc_final: 0.8669 (m) REVERT: A 2321 GLN cc_start: 0.8010 (mm110) cc_final: 0.7800 (tp-100) REVERT: A 2449 VAL cc_start: 0.6792 (p) cc_final: 0.6576 (p) REVERT: A 2680 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7529 (ptpt) REVERT: A 2815 SER cc_start: 0.8376 (m) cc_final: 0.8036 (t) REVERT: A 2873 MET cc_start: 0.7949 (mmm) cc_final: 0.7733 (mmt) REVERT: A 3195 GLU cc_start: 0.8130 (pt0) cc_final: 0.7690 (mm-30) REVERT: A 3374 ASN cc_start: 0.6584 (t0) cc_final: 0.6045 (p0) REVERT: A 3502 MET cc_start: 0.8339 (mtm) cc_final: 0.8087 (mtm) REVERT: A 3656 MET cc_start: 0.8005 (mtp) cc_final: 0.7765 (mtp) REVERT: A 3690 MET cc_start: 0.8322 (mpt) cc_final: 0.8097 (mtt) REVERT: A 4112 GLN cc_start: 0.8519 (tt0) cc_final: 0.7980 (tm-30) REVERT: A 4296 ILE cc_start: 0.8639 (mt) cc_final: 0.8419 (mt) REVERT: B 1278 LEU cc_start: 0.8345 (mm) cc_final: 0.8137 (mm) REVERT: B 1373 GLU cc_start: 0.8456 (tt0) cc_final: 0.7808 (mm-30) REVERT: B 1397 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7686 (tt) REVERT: B 1439 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7335 (mt-10) REVERT: B 1907 MET cc_start: 0.8572 (mmp) cc_final: 0.8325 (mmm) REVERT: B 1988 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8636 (mp) REVERT: B 2272 LEU cc_start: 0.7751 (mt) cc_final: 0.7505 (tp) REVERT: B 2319 SER cc_start: 0.8918 (p) cc_final: 0.8655 (m) REVERT: B 2321 GLN cc_start: 0.7973 (mm110) cc_final: 0.7729 (tp-100) REVERT: B 2815 SER cc_start: 0.8254 (m) cc_final: 0.7905 (t) REVERT: B 3374 ASN cc_start: 0.6543 (t0) cc_final: 0.5972 (p0) REVERT: B 3502 MET cc_start: 0.8150 (mtm) cc_final: 0.7800 (mtm) REVERT: B 3579 MET cc_start: 0.8641 (mmm) cc_final: 0.8431 (mmm) REVERT: B 3656 MET cc_start: 0.7864 (mtp) cc_final: 0.7646 (mtp) REVERT: B 3690 MET cc_start: 0.8326 (mpt) cc_final: 0.8049 (mtt) REVERT: B 4112 GLN cc_start: 0.8574 (tt0) cc_final: 0.8076 (tm-30) outliers start: 76 outliers final: 30 residues processed: 555 average time/residue: 0.2598 time to fit residues: 240.9535 Evaluate side-chains 390 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 355 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1747 GLU Chi-restraints excluded: chain A residue 1848 ILE 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 2178 HIS Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2680 LYS Chi-restraints excluded: chain A residue 2884 SER Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3294 HIS 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 B residue 1397 ILE 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 2178 HIS Chi-restraints excluded: chain B residue 2412 LEU 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 3294 HIS 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 3688 SER Chi-restraints excluded: chain B residue 3728 SER Chi-restraints excluded: chain B residue 3791 VAL 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 ************** Weight determination summary: number of chunks: 550 random chunks: chunk 491 optimal weight: 0.9990 chunk 543 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 515 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 213 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 313 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1900 GLN ** A2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3294 HIS A4045 ASN A4139 GLN B1792 ASN B1900 GLN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3294 HIS B3552 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.095459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.080621 restraints weight = 138813.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082555 restraints weight = 79252.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.083839 restraints weight = 53503.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.084706 restraints weight = 40753.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.085296 restraints weight = 33648.064| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43944 Z= 0.128 Angle : 0.637 10.549 59704 Z= 0.317 Chirality : 0.042 0.204 6764 Planarity : 0.004 0.048 7660 Dihedral : 7.798 166.688 6024 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.89 % Allowed : 11.23 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.11), residues: 5472 helix: 0.36 (0.09), residues: 2972 sheet: -1.31 (0.24), residues: 472 loop : -2.39 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2237 TYR 0.017 0.001 TYR A2162 PHE 0.023 0.001 PHE B2493 TRP 0.036 0.001 TRP B2502 HIS 0.007 0.001 HIS B3294 Details of bonding type rmsd covalent geometry : bond 0.00279 (43942) covalent geometry : angle 0.63726 (59704) hydrogen bonds : bond 0.04295 ( 2156) hydrogen bonds : angle 4.26334 ( 6318) Misc. bond : bond 0.00063 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 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 485 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 399 time to evaluate : 1.728 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: A 1278 LEU cc_start: 0.8517 (mm) cc_final: 0.8193 (mm) REVERT: A 1373 GLU cc_start: 0.8363 (tt0) cc_final: 0.7633 (mm-30) REVERT: A 1397 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7427 (pp) REVERT: A 1817 MET cc_start: 0.8518 (mtp) cc_final: 0.8286 (mmm) REVERT: A 1937 ASP cc_start: 0.7756 (p0) cc_final: 0.7006 (t0) REVERT: A 1988 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8524 (mt) REVERT: A 2268 MET cc_start: 0.7708 (mmp) cc_final: 0.7382 (tpp) REVERT: A 2319 SER cc_start: 0.8913 (p) cc_final: 0.8537 (m) REVERT: A 2321 GLN cc_start: 0.8088 (mm110) cc_final: 0.7739 (tp-100) REVERT: A 2449 VAL cc_start: 0.6674 (p) cc_final: 0.6440 (p) REVERT: A 2741 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7617 (mm) REVERT: A 2815 SER cc_start: 0.8413 (m) cc_final: 0.8138 (t) REVERT: A 3195 GLU cc_start: 0.8232 (pt0) cc_final: 0.7712 (mm-30) REVERT: A 3275 ARG cc_start: 0.7395 (mmp-170) cc_final: 0.7112 (mmp80) REVERT: A 3329 MET cc_start: 0.8572 (tpp) cc_final: 0.8135 (tpp) REVERT: A 3374 ASN cc_start: 0.6695 (t0) cc_final: 0.6103 (p0) REVERT: A 3502 MET cc_start: 0.8309 (mtm) cc_final: 0.8027 (mtm) REVERT: A 3656 MET cc_start: 0.8250 (mtp) cc_final: 0.8040 (mtp) REVERT: A 3821 LEU cc_start: 0.7597 (pp) cc_final: 0.7147 (tt) REVERT: A 4112 GLN cc_start: 0.8421 (tt0) cc_final: 0.7880 (tm-30) REVERT: A 4296 ILE cc_start: 0.8519 (mt) cc_final: 0.8239 (mt) REVERT: B 1278 LEU cc_start: 0.8494 (mm) cc_final: 0.8182 (mm) REVERT: B 1373 GLU cc_start: 0.8361 (tt0) cc_final: 0.7579 (mm-30) REVERT: B 1397 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7381 (pp) REVERT: B 1937 ASP cc_start: 0.7759 (p0) cc_final: 0.7038 (t0) REVERT: B 1988 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8532 (mt) REVERT: B 2319 SER cc_start: 0.8890 (p) cc_final: 0.8596 (m) REVERT: B 2321 GLN cc_start: 0.8143 (mm110) cc_final: 0.7810 (tp-100) REVERT: B 2449 VAL cc_start: 0.6681 (p) cc_final: 0.6437 (p) REVERT: B 2741 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7663 (mm) REVERT: B 2815 SER cc_start: 0.8369 (m) cc_final: 0.8079 (t) REVERT: B 3512 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8650 (tp) REVERT: B 3690 MET cc_start: 0.8304 (mpt) cc_final: 0.8073 (mtt) REVERT: B 4112 GLN cc_start: 0.8316 (tt0) cc_final: 0.7795 (tm-30) REVERT: B 4296 ILE cc_start: 0.8675 (mt) cc_final: 0.8411 (mt) outliers start: 86 outliers final: 45 residues processed: 456 average time/residue: 0.2178 time to fit residues: 171.2730 Evaluate side-chains 383 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 331 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1434 ASP Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1747 GLU Chi-restraints excluded: chain A residue 1848 ILE 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 2178 HIS Chi-restraints excluded: chain A residue 2476 VAL Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2564 ILE Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2741 LEU Chi-restraints excluded: chain A residue 2773 GLN Chi-restraints excluded: chain A residue 2884 SER Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3294 HIS Chi-restraints excluded: chain A residue 3357 ASP Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3408 ILE Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3701 LYS Chi-restraints excluded: chain A residue 3728 SER Chi-restraints excluded: chain A residue 3766 MET Chi-restraints excluded: chain A residue 4116 SER Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1415 LEU Chi-restraints excluded: chain B residue 1533 LEU 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 1947 PHE Chi-restraints excluded: chain B residue 1988 LEU Chi-restraints excluded: chain B residue 2178 HIS Chi-restraints excluded: chain B residue 2412 LEU Chi-restraints excluded: chain B residue 2476 VAL Chi-restraints excluded: chain B residue 2503 VAL Chi-restraints excluded: chain B residue 2556 PHE Chi-restraints excluded: chain B residue 2741 LEU Chi-restraints excluded: chain B residue 2884 SER Chi-restraints excluded: chain B residue 3294 HIS Chi-restraints excluded: chain B residue 3408 ILE Chi-restraints excluded: chain B residue 3505 ILE Chi-restraints excluded: chain B residue 3512 ILE Chi-restraints excluded: chain B residue 3688 SER Chi-restraints excluded: chain B residue 3718 LEU Chi-restraints excluded: chain B residue 3727 ILE Chi-restraints excluded: chain B residue 3728 SER Chi-restraints excluded: chain B residue 3766 MET Chi-restraints excluded: chain B residue 4094 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 101 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 372 optimal weight: 6.9990 chunk 296 optimal weight: 2.9990 chunk 375 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 485 optimal weight: 3.9990 chunk 382 optimal weight: 0.0070 chunk 272 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1344 HIS A1614 ASN ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3327 GLN A4058 HIS B1614 ASN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3294 HIS B3327 GLN B3552 GLN B4058 HIS B4139 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.092001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077112 restraints weight = 142777.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.078952 restraints weight = 83179.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.080178 restraints weight = 57125.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081010 restraints weight = 43962.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.081519 restraints weight = 36656.915| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 43944 Z= 0.202 Angle : 0.698 11.973 59704 Z= 0.350 Chirality : 0.044 0.180 6764 Planarity : 0.004 0.047 7660 Dihedral : 7.859 178.930 6024 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.59 % Allowed : 12.44 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.11), residues: 5472 helix: 0.60 (0.09), residues: 2954 sheet: -1.38 (0.24), residues: 460 loop : -2.30 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1376 TYR 0.036 0.002 TYR B1338 PHE 0.021 0.002 PHE B2287 TRP 0.043 0.002 TRP A3589 HIS 0.011 0.002 HIS B3294 Details of bonding type rmsd covalent geometry : bond 0.00459 (43942) covalent geometry : angle 0.69844 (59704) hydrogen bonds : bond 0.04670 ( 2156) hydrogen bonds : angle 4.39363 ( 6318) Misc. bond : bond 0.00130 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 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 455 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 337 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1278 LEU cc_start: 0.8518 (mm) cc_final: 0.8192 (mm) REVERT: A 1373 GLU cc_start: 0.8541 (tt0) cc_final: 0.7844 (mm-30) REVERT: A 1397 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7535 (pp) REVERT: A 1507 MET cc_start: 0.8012 (tmm) cc_final: 0.7747 (tmm) REVERT: A 1907 MET cc_start: 0.8390 (mmm) cc_final: 0.8104 (tpp) REVERT: A 1937 ASP cc_start: 0.7858 (p0) cc_final: 0.7068 (t0) REVERT: A 1947 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: A 2008 MET cc_start: 0.7865 (mtt) cc_final: 0.7582 (mtt) REVERT: A 2319 SER cc_start: 0.9058 (p) cc_final: 0.8755 (m) REVERT: A 2406 MET cc_start: 0.7976 (ptp) cc_final: 0.7712 (ptp) REVERT: A 2741 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7635 (mm) REVERT: A 2815 SER cc_start: 0.8620 (m) cc_final: 0.8293 (t) REVERT: A 3195 GLU cc_start: 0.8295 (pt0) cc_final: 0.7999 (mm-30) REVERT: A 3275 ARG cc_start: 0.7303 (mmp-170) cc_final: 0.7021 (mmp80) REVERT: A 3374 ASN cc_start: 0.7441 (t0) cc_final: 0.6542 (p0) REVERT: A 3502 MET cc_start: 0.8331 (mtm) cc_final: 0.8068 (mtm) REVERT: A 3590 ASP cc_start: 0.8025 (t0) cc_final: 0.7616 (t0) REVERT: A 3656 MET cc_start: 0.8314 (mtp) cc_final: 0.8086 (mtp) REVERT: A 3718 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8491 (pp) REVERT: A 3732 ASP cc_start: 0.7808 (t0) cc_final: 0.7595 (t0) REVERT: A 4112 GLN cc_start: 0.8529 (tt0) cc_final: 0.7895 (tm-30) REVERT: A 4296 ILE cc_start: 0.8479 (mt) cc_final: 0.8176 (mt) REVERT: B 1278 LEU cc_start: 0.8496 (mm) cc_final: 0.8181 (mm) REVERT: B 1373 GLU cc_start: 0.8485 (tt0) cc_final: 0.7745 (mm-30) REVERT: B 1716 ASP cc_start: 0.6707 (m-30) cc_final: 0.5573 (t70) REVERT: B 1937 ASP cc_start: 0.7851 (p0) cc_final: 0.7048 (t0) REVERT: B 1958 GLN cc_start: 0.7994 (mt0) cc_final: 0.7372 (tp-100) REVERT: B 2319 SER cc_start: 0.9026 (p) cc_final: 0.8768 (m) REVERT: B 2321 GLN cc_start: 0.8089 (mm110) cc_final: 0.7881 (tp-100) REVERT: B 2637 MET cc_start: 0.8666 (tpp) cc_final: 0.8387 (tpp) REVERT: B 2741 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7539 (mm) REVERT: B 2815 SER cc_start: 0.8570 (m) cc_final: 0.8250 (t) REVERT: B 3329 MET cc_start: 0.8633 (tpp) cc_final: 0.8114 (tpp) REVERT: B 3374 ASN cc_start: 0.7048 (t0) cc_final: 0.6371 (p0) REVERT: B 4085 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8259 (ttm-80) REVERT: B 4112 GLN cc_start: 0.8389 (tt0) cc_final: 0.7800 (tm-30) REVERT: B 4296 ILE cc_start: 0.8585 (mt) cc_final: 0.8318 (mt) outliers start: 118 outliers final: 68 residues processed: 426 average time/residue: 0.2183 time to fit residues: 160.3496 Evaluate side-chains 369 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 295 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1374 ASP Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1616 ILE Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1747 GLU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain A residue 1947 PHE Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2022 ILE Chi-restraints excluded: chain A residue 2078 MET Chi-restraints excluded: chain A residue 2178 HIS Chi-restraints excluded: chain A residue 2336 MET Chi-restraints excluded: chain A residue 2476 VAL Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2564 ILE Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2680 LYS Chi-restraints excluded: chain A residue 2741 LEU Chi-restraints excluded: chain A residue 2884 SER Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3293 THR Chi-restraints excluded: chain A residue 3294 HIS Chi-restraints excluded: chain A residue 3308 SER Chi-restraints excluded: chain A residue 3357 ASP Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3408 ILE Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3701 LYS Chi-restraints excluded: chain A residue 3718 LEU Chi-restraints excluded: chain A residue 3728 SER Chi-restraints excluded: chain A residue 3766 MET Chi-restraints excluded: chain A residue 3846 SER Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4116 SER Chi-restraints excluded: chain B residue 1374 ASP Chi-restraints excluded: chain B residue 1415 LEU Chi-restraints excluded: chain B residue 1434 ASP Chi-restraints excluded: chain B residue 1533 LEU Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 1616 ILE Chi-restraints excluded: chain B residue 1618 VAL Chi-restraints excluded: chain B residue 1747 GLU Chi-restraints excluded: chain B residue 1791 MET Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1947 PHE Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2178 HIS Chi-restraints excluded: chain B residue 2352 GLU Chi-restraints excluded: chain B residue 2412 LEU Chi-restraints excluded: chain B residue 2503 VAL Chi-restraints excluded: chain B residue 2556 PHE Chi-restraints excluded: chain B residue 2568 MET Chi-restraints excluded: chain B residue 2680 LYS Chi-restraints excluded: chain B residue 2741 LEU Chi-restraints excluded: chain B residue 2884 SER Chi-restraints excluded: chain B residue 3294 HIS Chi-restraints excluded: chain B residue 3308 SER Chi-restraints excluded: chain B residue 3357 ASP Chi-restraints excluded: chain B residue 3370 LEU Chi-restraints excluded: chain B residue 3408 ILE Chi-restraints excluded: chain B residue 3505 ILE Chi-restraints excluded: chain B residue 3688 SER Chi-restraints excluded: chain B residue 3718 LEU Chi-restraints excluded: chain B residue 3728 SER Chi-restraints excluded: chain B residue 3766 MET Chi-restraints excluded: chain B residue 3846 SER Chi-restraints excluded: chain B residue 4058 HIS Chi-restraints excluded: chain B residue 4085 ARG Chi-restraints excluded: chain B residue 4094 LEU Chi-restraints excluded: chain B residue 4116 SER Chi-restraints excluded: chain B residue 4144 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 277 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 376 optimal weight: 7.9990 chunk 438 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 352 optimal weight: 4.9990 chunk 381 optimal weight: 0.0770 chunk 395 optimal weight: 0.1980 chunk 314 optimal weight: 4.9990 chunk 136 optimal weight: 0.0010 chunk 188 optimal weight: 0.9990 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1784 ASN A1905 ASN ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2097 HIS ** A2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3327 GLN B1784 ASN B1905 ASN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2097 HIS ** B2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.095585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080685 restraints weight = 138861.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.082642 restraints weight = 79308.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.083939 restraints weight = 53563.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.084806 restraints weight = 40701.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.085370 restraints weight = 33693.239| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 43944 Z= 0.109 Angle : 0.601 10.791 59704 Z= 0.295 Chirality : 0.041 0.243 6764 Planarity : 0.004 0.049 7660 Dihedral : 7.215 172.934 6022 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.18 % Allowed : 13.27 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.12), residues: 5472 helix: 1.02 (0.10), residues: 2972 sheet: -1.13 (0.24), residues: 480 loop : -2.13 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B2237 TYR 0.015 0.001 TYR B2509 PHE 0.027 0.001 PHE B2493 TRP 0.037 0.001 TRP A3589 HIS 0.009 0.001 HIS B3294 Details of bonding type rmsd covalent geometry : bond 0.00225 (43942) covalent geometry : angle 0.60063 (59704) hydrogen bonds : bond 0.03803 ( 2156) hydrogen bonds : angle 4.00505 ( 6318) Misc. bond : bond 0.00081 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 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 471 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 372 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1278 LEU cc_start: 0.8453 (mm) cc_final: 0.8101 (mm) REVERT: A 1373 GLU cc_start: 0.8486 (tt0) cc_final: 0.7765 (mm-30) REVERT: A 1507 MET cc_start: 0.7944 (tmm) cc_final: 0.7680 (tmt) REVERT: A 1724 MET cc_start: 0.7599 (mmp) cc_final: 0.7228 (mmp) REVERT: A 1937 ASP cc_start: 0.7768 (p0) cc_final: 0.7026 (t0) REVERT: A 2008 MET cc_start: 0.7654 (mtt) cc_final: 0.7347 (mtt) REVERT: A 2319 SER cc_start: 0.9001 (p) cc_final: 0.8574 (m) REVERT: A 2775 ASN cc_start: 0.7409 (m-40) cc_final: 0.7115 (m-40) REVERT: A 2815 SER cc_start: 0.8491 (m) cc_final: 0.8215 (t) REVERT: A 3195 GLU cc_start: 0.8272 (pt0) cc_final: 0.7985 (mm-30) REVERT: A 3329 MET cc_start: 0.8720 (tpp) cc_final: 0.8454 (tpp) REVERT: A 3590 ASP cc_start: 0.8120 (t0) cc_final: 0.7719 (t70) REVERT: A 3732 ASP cc_start: 0.7702 (t0) cc_final: 0.7462 (t0) REVERT: A 3810 THR cc_start: 0.8728 (m) cc_final: 0.8196 (p) REVERT: A 4112 GLN cc_start: 0.8373 (tt0) cc_final: 0.7832 (tm-30) REVERT: A 4250 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7353 (mpp) REVERT: A 4296 ILE cc_start: 0.8329 (mt) cc_final: 0.8016 (mt) REVERT: B 1278 LEU cc_start: 0.8476 (mm) cc_final: 0.8169 (mm) REVERT: B 1373 GLU cc_start: 0.8456 (tt0) cc_final: 0.7720 (mm-30) REVERT: B 1644 MET cc_start: 0.5915 (ttm) cc_final: 0.5373 (tpp) REVERT: B 1716 ASP cc_start: 0.6413 (m-30) cc_final: 0.5292 (t0) REVERT: B 1724 MET cc_start: 0.7630 (mmp) cc_final: 0.7234 (mmp) REVERT: B 1937 ASP cc_start: 0.7757 (p0) cc_final: 0.7036 (t0) REVERT: B 1958 GLN cc_start: 0.7991 (mt0) cc_final: 0.7369 (tp-100) REVERT: B 2319 SER cc_start: 0.8950 (p) cc_final: 0.8563 (m) REVERT: B 2446 LEU cc_start: 0.7459 (tt) cc_final: 0.6569 (mt) REVERT: B 2773 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: B 2815 SER cc_start: 0.8471 (m) cc_final: 0.8221 (t) REVERT: B 2822 MET cc_start: 0.7619 (ptp) cc_final: 0.7415 (ptm) REVERT: B 3329 MET cc_start: 0.8601 (tpp) cc_final: 0.8340 (tpp) REVERT: B 3810 THR cc_start: 0.8721 (m) cc_final: 0.8197 (p) REVERT: B 4112 GLN cc_start: 0.8247 (tt0) cc_final: 0.7770 (tm-30) REVERT: B 4296 ILE cc_start: 0.8441 (mt) cc_final: 0.8092 (mt) outliers start: 99 outliers final: 56 residues processed: 451 average time/residue: 0.2206 time to fit residues: 171.5881 Evaluate side-chains 370 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 312 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1374 ASP Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1434 ASP Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1616 ILE Chi-restraints excluded: chain A residue 1747 GLU Chi-restraints excluded: chain A residue 1804 LEU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain A residue 1976 VAL Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2178 HIS Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2564 ILE Chi-restraints excluded: chain A residue 2680 LYS Chi-restraints excluded: chain A residue 3285 SER Chi-restraints excluded: chain A residue 3294 HIS Chi-restraints excluded: chain A residue 3370 LEU 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 3766 MET Chi-restraints excluded: chain A residue 3846 SER Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4116 SER Chi-restraints excluded: chain A residue 4144 LEU Chi-restraints excluded: chain A residue 4250 MET Chi-restraints excluded: chain B residue 1533 LEU Chi-restraints excluded: chain B residue 1616 ILE Chi-restraints excluded: chain B residue 1747 GLU Chi-restraints excluded: chain B residue 1804 LEU Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1947 PHE Chi-restraints excluded: chain B residue 1976 VAL Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2026 THR Chi-restraints excluded: chain B residue 2178 HIS Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2412 LEU 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 2773 GLN Chi-restraints excluded: chain B residue 2884 SER Chi-restraints excluded: chain B residue 3285 SER Chi-restraints excluded: chain B residue 3294 HIS Chi-restraints excluded: chain B residue 3370 LEU Chi-restraints excluded: chain B residue 3408 ILE Chi-restraints excluded: chain B residue 3505 ILE Chi-restraints excluded: chain B residue 3688 SER Chi-restraints excluded: chain B residue 3718 LEU Chi-restraints excluded: chain B residue 3766 MET Chi-restraints excluded: chain B residue 3846 SER Chi-restraints excluded: chain B residue 4058 HIS Chi-restraints excluded: chain B residue 4094 LEU Chi-restraints excluded: chain B residue 4116 SER Chi-restraints excluded: chain B residue 4144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 142 optimal weight: 0.8980 chunk 500 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 257 optimal weight: 0.0050 chunk 488 optimal weight: 0.8980 chunk 434 optimal weight: 0.3980 chunk 167 optimal weight: 0.2980 chunk 466 optimal weight: 10.0000 chunk 475 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1344 HIS ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2321 GLN ** B2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.097047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.082830 restraints weight = 138606.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.084562 restraints weight = 83397.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.085750 restraints weight = 58563.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.086552 restraints weight = 45699.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087016 restraints weight = 38324.668| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 43944 Z= 0.104 Angle : 0.593 11.658 59704 Z= 0.288 Chirality : 0.041 0.217 6764 Planarity : 0.003 0.048 7660 Dihedral : 6.722 149.044 6020 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.93 % Allowed : 13.96 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.12), residues: 5472 helix: 1.25 (0.10), residues: 2982 sheet: -1.01 (0.24), residues: 482 loop : -2.03 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2083 TYR 0.014 0.001 TYR A3558 PHE 0.027 0.001 PHE A1849 TRP 0.036 0.001 TRP B2502 HIS 0.007 0.001 HIS A3919 Details of bonding type rmsd covalent geometry : bond 0.00221 (43942) covalent geometry : angle 0.59268 (59704) hydrogen bonds : bond 0.03522 ( 2156) hydrogen bonds : angle 3.86872 ( 6318) Misc. bond : bond 0.00069 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 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 447 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 359 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1278 LEU cc_start: 0.8243 (mm) cc_final: 0.7944 (mm) REVERT: A 1373 GLU cc_start: 0.8367 (tt0) cc_final: 0.7799 (mm-30) REVERT: A 1724 MET cc_start: 0.7525 (mmp) cc_final: 0.7223 (mmp) REVERT: A 1937 ASP cc_start: 0.7436 (p0) cc_final: 0.6884 (t0) REVERT: A 1958 GLN cc_start: 0.7863 (mt0) cc_final: 0.7365 (tp-100) REVERT: A 2110 MET cc_start: 0.8550 (ppp) cc_final: 0.7112 (ppp) REVERT: A 2319 SER cc_start: 0.8956 (p) cc_final: 0.8539 (m) REVERT: A 2741 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7601 (mm) REVERT: A 2773 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: A 2822 MET cc_start: 0.7727 (ptp) cc_final: 0.7460 (ptm) REVERT: A 3195 GLU cc_start: 0.8190 (pt0) cc_final: 0.7943 (mm-30) REVERT: A 3336 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8180 (mt) REVERT: A 3590 ASP cc_start: 0.7653 (t0) cc_final: 0.7385 (t0) REVERT: A 3732 ASP cc_start: 0.7518 (t0) cc_final: 0.7220 (t0) REVERT: A 3810 THR cc_start: 0.8791 (m) cc_final: 0.8296 (p) REVERT: A 4009 MET cc_start: 0.7166 (mmm) cc_final: 0.6936 (mmm) REVERT: A 4112 GLN cc_start: 0.8319 (tt0) cc_final: 0.7837 (tm-30) REVERT: A 4296 ILE cc_start: 0.8355 (mt) cc_final: 0.8053 (mt) REVERT: B 1278 LEU cc_start: 0.8244 (mm) cc_final: 0.7990 (mm) REVERT: B 1373 GLU cc_start: 0.8450 (tt0) cc_final: 0.7805 (mm-30) REVERT: B 1397 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6898 (pp) REVERT: B 1644 MET cc_start: 0.5965 (ttm) cc_final: 0.5661 (tpp) REVERT: B 1716 ASP cc_start: 0.6400 (m-30) cc_final: 0.6122 (m-30) REVERT: B 1724 MET cc_start: 0.7565 (mmp) cc_final: 0.7216 (mmp) REVERT: B 1937 ASP cc_start: 0.7464 (p0) cc_final: 0.6894 (t0) REVERT: B 1958 GLN cc_start: 0.7783 (mt0) cc_final: 0.7308 (tp-100) REVERT: B 2319 SER cc_start: 0.8926 (p) cc_final: 0.8529 (m) REVERT: B 2741 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7612 (mm) REVERT: B 2815 SER cc_start: 0.8396 (m) cc_final: 0.8175 (t) REVERT: B 3336 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8298 (mt) REVERT: B 3810 THR cc_start: 0.8827 (m) cc_final: 0.8355 (p) REVERT: B 4112 GLN cc_start: 0.8262 (tt0) cc_final: 0.7867 (tm-30) REVERT: B 4296 ILE cc_start: 0.8359 (mt) cc_final: 0.8055 (mt) outliers start: 88 outliers final: 58 residues processed: 429 average time/residue: 0.2073 time to fit residues: 154.3323 Evaluate side-chains 378 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 314 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1374 ASP Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1747 GLU Chi-restraints excluded: chain A residue 1804 LEU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain A residue 1991 MET Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2090 VAL Chi-restraints excluded: chain A residue 2178 HIS Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2564 ILE Chi-restraints excluded: chain A residue 2680 LYS Chi-restraints excluded: chain A residue 2741 LEU Chi-restraints excluded: chain A residue 2773 GLN Chi-restraints excluded: chain A residue 2884 SER Chi-restraints excluded: chain A residue 3285 SER Chi-restraints excluded: chain A residue 3308 SER Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3357 ASP Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3408 ILE Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3688 SER Chi-restraints excluded: chain A residue 3728 SER Chi-restraints excluded: chain A residue 3766 MET Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4116 SER Chi-restraints excluded: chain A residue 4144 LEU Chi-restraints excluded: chain A residue 4245 VAL Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1434 ASP Chi-restraints excluded: chain B residue 1533 LEU Chi-restraints excluded: chain B residue 1747 GLU Chi-restraints excluded: chain B residue 1804 LEU Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1947 PHE Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2026 THR Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2178 HIS Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2412 LEU Chi-restraints excluded: chain B residue 2427 LEU Chi-restraints excluded: chain B residue 2503 VAL Chi-restraints excluded: chain B residue 2680 LYS Chi-restraints excluded: chain B residue 2741 LEU Chi-restraints excluded: chain B residue 2884 SER Chi-restraints excluded: chain B residue 3285 SER Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain B residue 3370 LEU Chi-restraints excluded: chain B residue 3408 ILE Chi-restraints excluded: chain B residue 3505 ILE Chi-restraints excluded: chain B residue 3688 SER Chi-restraints excluded: chain B residue 3718 LEU Chi-restraints excluded: chain B residue 3728 SER Chi-restraints excluded: chain B residue 3766 MET Chi-restraints excluded: chain B residue 4058 HIS Chi-restraints excluded: chain B residue 4094 LEU Chi-restraints excluded: chain B residue 4144 LEU Chi-restraints excluded: chain B residue 4245 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 272 optimal weight: 3.9990 chunk 280 optimal weight: 8.9990 chunk 134 optimal weight: 0.7980 chunk 442 optimal weight: 7.9990 chunk 325 optimal weight: 0.6980 chunk 237 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 323 optimal weight: 6.9990 chunk 376 optimal weight: 0.9990 chunk 476 optimal weight: 0.0270 chunk 339 optimal weight: 8.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3305 GLN B1305 ASN B1614 ASN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2719 HIS ** B2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.097349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.083064 restraints weight = 138297.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.084787 restraints weight = 84092.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.085946 restraints weight = 59403.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.086739 restraints weight = 46586.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.087195 restraints weight = 39220.967| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 43944 Z= 0.106 Angle : 0.595 11.444 59704 Z= 0.288 Chirality : 0.041 0.192 6764 Planarity : 0.003 0.047 7660 Dihedral : 6.468 133.169 6020 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.15 % Allowed : 14.22 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.12), residues: 5472 helix: 1.40 (0.10), residues: 2992 sheet: -0.88 (0.24), residues: 496 loop : -1.93 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4279 TYR 0.019 0.001 TYR A2865 PHE 0.028 0.001 PHE A2493 TRP 0.054 0.001 TRP B2502 HIS 0.005 0.001 HIS A3919 Details of bonding type rmsd covalent geometry : bond 0.00227 (43942) covalent geometry : angle 0.59520 (59704) hydrogen bonds : bond 0.03428 ( 2156) hydrogen bonds : angle 3.79936 ( 6318) Misc. bond : bond 0.00078 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 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 448 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 350 time to evaluate : 1.615 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: A 1278 LEU cc_start: 0.8204 (mm) cc_final: 0.7949 (mm) REVERT: A 1373 GLU cc_start: 0.8358 (tt0) cc_final: 0.7726 (mm-30) REVERT: A 1397 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6741 (pp) REVERT: A 1724 MET cc_start: 0.7526 (mmp) cc_final: 0.7157 (mmp) REVERT: A 1937 ASP cc_start: 0.7423 (p0) cc_final: 0.6894 (t0) REVERT: A 1958 GLN cc_start: 0.7857 (mt0) cc_final: 0.7376 (tp-100) REVERT: A 2319 SER cc_start: 0.8936 (p) cc_final: 0.8511 (m) REVERT: A 2336 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7502 (mmm) REVERT: A 2347 ARG cc_start: 0.8069 (ttm170) cc_final: 0.7832 (ttm170) REVERT: A 2551 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8949 (tp) REVERT: A 2741 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7571 (mm) REVERT: A 2773 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: A 3195 GLU cc_start: 0.8181 (pt0) cc_final: 0.7936 (mm-30) REVERT: A 3336 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8251 (mt) REVERT: A 3590 ASP cc_start: 0.7501 (t0) cc_final: 0.7298 (t0) REVERT: A 3732 ASP cc_start: 0.7496 (t0) cc_final: 0.7172 (t0) REVERT: A 3810 THR cc_start: 0.8872 (m) cc_final: 0.8423 (p) REVERT: A 4009 MET cc_start: 0.7202 (mmm) cc_final: 0.6996 (mmm) REVERT: A 4112 GLN cc_start: 0.8305 (tt0) cc_final: 0.7859 (tm-30) REVERT: A 4296 ILE cc_start: 0.8315 (mt) cc_final: 0.8007 (mt) REVERT: B 1278 LEU cc_start: 0.8387 (mm) cc_final: 0.8131 (mm) REVERT: B 1373 GLU cc_start: 0.8450 (tt0) cc_final: 0.7733 (mm-30) REVERT: B 1397 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6767 (pp) REVERT: B 1644 MET cc_start: 0.6035 (ttm) cc_final: 0.5786 (tpp) REVERT: B 1724 MET cc_start: 0.7534 (mmp) cc_final: 0.7197 (mmp) REVERT: B 1937 ASP cc_start: 0.7505 (p0) cc_final: 0.6841 (t0) REVERT: B 1958 GLN cc_start: 0.7690 (mt0) cc_final: 0.7360 (tp-100) REVERT: B 2319 SER cc_start: 0.8917 (p) cc_final: 0.8529 (m) REVERT: B 2557 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7945 (mm-40) REVERT: B 2741 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7584 (mm) REVERT: B 2815 SER cc_start: 0.8421 (m) cc_final: 0.8218 (t) REVERT: B 2823 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6687 (mt) REVERT: B 3336 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8324 (mt) REVERT: B 3810 THR cc_start: 0.8861 (m) cc_final: 0.8427 (p) REVERT: B 4112 GLN cc_start: 0.8243 (tt0) cc_final: 0.7878 (tm-30) REVERT: B 4296 ILE cc_start: 0.8362 (mt) cc_final: 0.8057 (mt) outliers start: 98 outliers final: 67 residues processed: 422 average time/residue: 0.2315 time to fit residues: 169.9984 Evaluate side-chains 393 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 315 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1374 ASP Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1434 ASP Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1747 GLU Chi-restraints excluded: chain A residue 1804 LEU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1849 PHE Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain A residue 1991 MET Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2064 GLU Chi-restraints excluded: chain A residue 2178 HIS Chi-restraints excluded: chain A residue 2336 MET Chi-restraints excluded: chain A residue 2352 GLU Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2551 ILE Chi-restraints excluded: chain A residue 2564 ILE Chi-restraints excluded: chain A residue 2680 LYS Chi-restraints excluded: chain A residue 2741 LEU Chi-restraints excluded: chain A residue 2773 GLN Chi-restraints excluded: chain A residue 2884 SER Chi-restraints excluded: chain A residue 3308 SER Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3393 THR Chi-restraints excluded: chain A residue 3408 ILE Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3626 VAL Chi-restraints excluded: chain A residue 3688 SER Chi-restraints excluded: chain A residue 3728 SER Chi-restraints excluded: chain A residue 3766 MET Chi-restraints excluded: chain A residue 3846 SER Chi-restraints excluded: chain A residue 4116 SER Chi-restraints excluded: chain A residue 4144 LEU Chi-restraints excluded: chain A residue 4245 VAL Chi-restraints excluded: chain B residue 1374 ASP Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1415 LEU Chi-restraints excluded: chain B residue 1476 MET Chi-restraints excluded: chain B residue 1533 LEU Chi-restraints excluded: chain B residue 1747 GLU Chi-restraints excluded: chain B residue 1804 LEU Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1947 PHE Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2026 THR Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2178 HIS Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2412 LEU Chi-restraints excluded: chain B residue 2427 LEU Chi-restraints excluded: chain B residue 2503 VAL Chi-restraints excluded: chain B residue 2557 GLN Chi-restraints excluded: chain B residue 2680 LYS Chi-restraints excluded: chain B residue 2741 LEU Chi-restraints excluded: chain B residue 2823 LEU Chi-restraints excluded: chain B residue 2884 SER Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain B residue 3370 LEU Chi-restraints excluded: chain B residue 3393 THR Chi-restraints excluded: chain B residue 3408 ILE Chi-restraints excluded: chain B residue 3505 ILE Chi-restraints excluded: chain B residue 3626 VAL Chi-restraints excluded: chain B residue 3688 SER Chi-restraints excluded: chain B residue 3718 LEU Chi-restraints excluded: chain B residue 3728 SER Chi-restraints excluded: chain B residue 3766 MET Chi-restraints excluded: chain B residue 3846 SER Chi-restraints excluded: chain B residue 4058 HIS Chi-restraints excluded: chain B residue 4094 LEU Chi-restraints excluded: chain B residue 4116 SER Chi-restraints excluded: chain B residue 4144 LEU Chi-restraints excluded: chain B residue 4245 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 223 optimal weight: 0.8980 chunk 193 optimal weight: 30.0000 chunk 33 optimal weight: 0.2980 chunk 185 optimal weight: 0.0370 chunk 103 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 268 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 396 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 378 optimal weight: 7.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1614 ASN ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2623 GLN ** A2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2623 GLN ** B2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.097331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.082888 restraints weight = 138879.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.084633 restraints weight = 85139.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.085782 restraints weight = 60286.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.086564 restraints weight = 47455.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.087027 restraints weight = 40155.770| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 43944 Z= 0.105 Angle : 0.592 11.139 59704 Z= 0.286 Chirality : 0.041 0.242 6764 Planarity : 0.003 0.046 7660 Dihedral : 6.222 126.034 6020 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.00 % Allowed : 14.99 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.12), residues: 5472 helix: 1.51 (0.10), residues: 2994 sheet: -0.81 (0.24), residues: 496 loop : -1.89 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B4279 TYR 0.016 0.001 TYR A3558 PHE 0.041 0.001 PHE B2768 TRP 0.052 0.001 TRP B2502 HIS 0.006 0.001 HIS A3919 Details of bonding type rmsd covalent geometry : bond 0.00229 (43942) covalent geometry : angle 0.59223 (59704) hydrogen bonds : bond 0.03332 ( 2156) hydrogen bonds : angle 3.77045 ( 6318) Misc. bond : bond 0.00061 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 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 435 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 344 time to evaluate : 1.598 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: A 1373 GLU cc_start: 0.8368 (tt0) cc_final: 0.7760 (mm-30) REVERT: A 1397 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6585 (pp) REVERT: A 1724 MET cc_start: 0.7520 (mmp) cc_final: 0.7198 (mmp) REVERT: A 1937 ASP cc_start: 0.7481 (p0) cc_final: 0.6841 (t0) REVERT: A 1958 GLN cc_start: 0.7837 (mt0) cc_final: 0.7401 (tp-100) REVERT: A 2319 SER cc_start: 0.8938 (p) cc_final: 0.8542 (m) REVERT: A 2336 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7426 (mmm) REVERT: A 2347 ARG cc_start: 0.8107 (ttm170) cc_final: 0.7849 (ttm170) REVERT: A 2551 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8905 (tp) REVERT: A 2741 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7569 (mm) REVERT: A 3336 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8132 (mt) REVERT: A 3590 ASP cc_start: 0.7511 (t0) cc_final: 0.7299 (t0) REVERT: A 3732 ASP cc_start: 0.7525 (t0) cc_final: 0.7211 (t0) REVERT: A 3810 THR cc_start: 0.8866 (m) cc_final: 0.8441 (p) REVERT: A 4009 MET cc_start: 0.7151 (mmm) cc_final: 0.6950 (mmm) REVERT: A 4020 ILE cc_start: 0.8223 (tt) cc_final: 0.7856 (tp) REVERT: A 4112 GLN cc_start: 0.8244 (tt0) cc_final: 0.7817 (tm-30) REVERT: A 4296 ILE cc_start: 0.8287 (mt) cc_final: 0.7981 (mt) REVERT: B 1278 LEU cc_start: 0.8394 (mm) cc_final: 0.8118 (mm) REVERT: B 1373 GLU cc_start: 0.8377 (tt0) cc_final: 0.7654 (mm-30) REVERT: B 1397 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6530 (pp) REVERT: B 1716 ASP cc_start: 0.6263 (m-30) cc_final: 0.5099 (t0) REVERT: B 1724 MET cc_start: 0.7549 (mmp) cc_final: 0.7239 (mmp) REVERT: B 1937 ASP cc_start: 0.7459 (p0) cc_final: 0.6844 (t0) REVERT: B 1958 GLN cc_start: 0.7721 (mt0) cc_final: 0.7460 (tp-100) REVERT: B 2319 SER cc_start: 0.8899 (p) cc_final: 0.8523 (m) REVERT: B 2741 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7681 (mm) REVERT: B 3336 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8268 (mt) REVERT: B 3810 THR cc_start: 0.8857 (m) cc_final: 0.8439 (p) REVERT: B 4112 GLN cc_start: 0.8239 (tt0) cc_final: 0.7884 (tm-30) REVERT: B 4296 ILE cc_start: 0.8338 (mt) cc_final: 0.8028 (mt) outliers start: 91 outliers final: 70 residues processed: 414 average time/residue: 0.2271 time to fit residues: 164.7521 Evaluate side-chains 388 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 310 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1374 ASP Chi-restraints excluded: chain A residue 1394 HIS Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1434 ASP Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1747 GLU Chi-restraints excluded: chain A residue 1804 LEU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1849 PHE Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain A residue 1991 MET Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2064 GLU Chi-restraints excluded: chain A residue 2090 VAL Chi-restraints excluded: chain A residue 2178 HIS Chi-restraints excluded: chain A residue 2336 MET Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2352 GLU Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2551 ILE Chi-restraints excluded: chain A residue 2564 ILE Chi-restraints excluded: chain A residue 2680 LYS Chi-restraints excluded: chain A residue 2689 GLN Chi-restraints excluded: chain A residue 2741 LEU Chi-restraints excluded: chain A residue 2884 SER Chi-restraints excluded: chain A residue 3308 SER Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3368 LEU Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3393 THR Chi-restraints excluded: chain A residue 3408 ILE Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3626 VAL Chi-restraints excluded: chain A residue 3688 SER Chi-restraints excluded: chain A residue 3728 SER Chi-restraints excluded: chain A residue 3766 MET Chi-restraints excluded: chain A residue 3846 SER Chi-restraints excluded: chain A residue 4116 SER Chi-restraints excluded: chain A residue 4144 LEU Chi-restraints excluded: chain A residue 4245 VAL Chi-restraints excluded: chain B residue 1374 ASP Chi-restraints excluded: chain B residue 1388 VAL Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1415 LEU Chi-restraints excluded: chain B residue 1434 ASP Chi-restraints excluded: chain B residue 1533 LEU Chi-restraints excluded: chain B residue 1747 GLU Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1947 PHE Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2026 THR Chi-restraints excluded: chain B residue 2064 GLU Chi-restraints excluded: chain B residue 2178 HIS Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2412 LEU Chi-restraints excluded: chain B residue 2427 LEU Chi-restraints excluded: chain B residue 2680 LYS Chi-restraints excluded: chain B residue 2741 LEU Chi-restraints excluded: chain B residue 2884 SER Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain B residue 3370 LEU Chi-restraints excluded: chain B residue 3393 THR Chi-restraints excluded: chain B residue 3408 ILE Chi-restraints excluded: chain B residue 3505 ILE Chi-restraints excluded: chain B residue 3626 VAL Chi-restraints excluded: chain B residue 3688 SER Chi-restraints excluded: chain B residue 3718 LEU Chi-restraints excluded: chain B residue 3728 SER Chi-restraints excluded: chain B residue 3766 MET Chi-restraints excluded: chain B residue 3846 SER Chi-restraints excluded: chain B residue 4094 LEU Chi-restraints excluded: chain B residue 4116 SER Chi-restraints excluded: chain B residue 4144 LEU Chi-restraints excluded: chain B residue 4245 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 20 optimal weight: 0.0000 chunk 37 optimal weight: 5.9990 chunk 335 optimal weight: 0.8980 chunk 287 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 308 optimal weight: 0.5980 chunk 239 optimal weight: 1.9990 chunk 511 optimal weight: 0.9980 chunk 368 optimal weight: 0.7980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2362 ASN A2719 HIS ** A2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.097911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.083577 restraints weight = 138194.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.085323 restraints weight = 84085.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.086483 restraints weight = 59355.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.087282 restraints weight = 46559.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.087833 restraints weight = 39155.342| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 43944 Z= 0.103 Angle : 0.602 12.401 59704 Z= 0.289 Chirality : 0.041 0.249 6764 Planarity : 0.003 0.047 7660 Dihedral : 5.957 126.566 6020 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.89 % Allowed : 15.34 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.12), residues: 5472 helix: 1.59 (0.10), residues: 2994 sheet: -0.74 (0.24), residues: 496 loop : -1.81 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A4279 TYR 0.014 0.001 TYR A2865 PHE 0.030 0.001 PHE A2493 TRP 0.052 0.001 TRP A2502 HIS 0.005 0.001 HIS A3919 Details of bonding type rmsd covalent geometry : bond 0.00222 (43942) covalent geometry : angle 0.60198 (59704) hydrogen bonds : bond 0.03290 ( 2156) hydrogen bonds : angle 3.73860 ( 6318) Misc. bond : bond 0.00037 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 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 430 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 344 time to evaluate : 1.994 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: A 1373 GLU cc_start: 0.8330 (tt0) cc_final: 0.7709 (mm-30) REVERT: A 1397 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6530 (pp) REVERT: A 1724 MET cc_start: 0.7505 (mmp) cc_final: 0.7189 (mmp) REVERT: A 1937 ASP cc_start: 0.7449 (p0) cc_final: 0.6855 (t0) REVERT: A 1958 GLN cc_start: 0.7826 (mt0) cc_final: 0.7401 (tp-100) REVERT: A 1991 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6827 (mtp) REVERT: A 2319 SER cc_start: 0.8926 (p) cc_final: 0.8519 (m) REVERT: A 2347 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7867 (ttm170) REVERT: A 2551 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8906 (tp) REVERT: A 2741 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7488 (mm) REVERT: A 3336 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8114 (mt) REVERT: A 3590 ASP cc_start: 0.7551 (t0) cc_final: 0.7351 (t0) REVERT: A 3732 ASP cc_start: 0.7647 (t0) cc_final: 0.7330 (t0) REVERT: A 3810 THR cc_start: 0.8851 (m) cc_final: 0.8432 (p) REVERT: A 4112 GLN cc_start: 0.8218 (tt0) cc_final: 0.7831 (tm-30) REVERT: A 4296 ILE cc_start: 0.8257 (mt) cc_final: 0.7937 (mt) REVERT: B 1278 LEU cc_start: 0.8390 (mm) cc_final: 0.8111 (mm) REVERT: B 1373 GLU cc_start: 0.8347 (tt0) cc_final: 0.7642 (mm-30) REVERT: B 1397 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6449 (pp) REVERT: B 1716 ASP cc_start: 0.6236 (m-30) cc_final: 0.5037 (t0) REVERT: B 1724 MET cc_start: 0.7533 (mmp) cc_final: 0.7233 (mmp) REVERT: B 1937 ASP cc_start: 0.7372 (p0) cc_final: 0.6829 (t0) REVERT: B 1958 GLN cc_start: 0.7695 (mt0) cc_final: 0.7413 (tp-100) REVERT: B 2319 SER cc_start: 0.8901 (p) cc_final: 0.8526 (m) REVERT: B 2454 LEU cc_start: 0.8021 (pp) cc_final: 0.6383 (pp) REVERT: B 2741 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7686 (mm) REVERT: B 3336 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8289 (mt) REVERT: B 3810 THR cc_start: 0.8849 (m) cc_final: 0.8403 (p) REVERT: B 4112 GLN cc_start: 0.8316 (tt0) cc_final: 0.7908 (tm-30) REVERT: B 4296 ILE cc_start: 0.8305 (mt) cc_final: 0.7997 (mt) outliers start: 86 outliers final: 65 residues processed: 413 average time/residue: 0.2395 time to fit residues: 173.1919 Evaluate side-chains 383 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 310 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1394 HIS Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1747 GLU Chi-restraints excluded: chain A residue 1804 LEU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1991 MET Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2090 VAL Chi-restraints excluded: chain A residue 2178 HIS Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain A residue 2551 ILE Chi-restraints excluded: chain A residue 2564 ILE Chi-restraints excluded: chain A residue 2680 LYS Chi-restraints excluded: chain A residue 2689 GLN Chi-restraints excluded: chain A residue 2741 LEU Chi-restraints excluded: chain A residue 2884 SER Chi-restraints excluded: chain A residue 3238 PHE Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3368 LEU Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3393 THR Chi-restraints excluded: chain A residue 3408 ILE Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3626 VAL Chi-restraints excluded: chain A residue 3688 SER Chi-restraints excluded: chain A residue 3728 SER Chi-restraints excluded: chain A residue 3766 MET Chi-restraints excluded: chain A residue 4116 SER Chi-restraints excluded: chain A residue 4144 LEU Chi-restraints excluded: chain A residue 4245 VAL Chi-restraints excluded: chain B residue 1374 ASP Chi-restraints excluded: chain B residue 1388 VAL Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1415 LEU Chi-restraints excluded: chain B residue 1434 ASP Chi-restraints excluded: chain B residue 1533 LEU Chi-restraints excluded: chain B residue 1747 GLU Chi-restraints excluded: chain B residue 1804 LEU Chi-restraints excluded: chain B residue 1947 PHE Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2026 THR Chi-restraints excluded: chain B residue 2064 GLU Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2178 HIS Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2352 GLU Chi-restraints excluded: chain B residue 2412 LEU Chi-restraints excluded: chain B residue 2427 LEU Chi-restraints excluded: chain B residue 2689 GLN Chi-restraints excluded: chain B residue 2741 LEU Chi-restraints excluded: chain B residue 2884 SER Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain B residue 3368 LEU Chi-restraints excluded: chain B residue 3370 LEU Chi-restraints excluded: chain B residue 3393 THR Chi-restraints excluded: chain B residue 3408 ILE Chi-restraints excluded: chain B residue 3505 ILE Chi-restraints excluded: chain B residue 3626 VAL Chi-restraints excluded: chain B residue 3688 SER Chi-restraints excluded: chain B residue 3718 LEU Chi-restraints excluded: chain B residue 3728 SER Chi-restraints excluded: chain B residue 3766 MET Chi-restraints excluded: chain B residue 3846 SER Chi-restraints excluded: chain B residue 4094 LEU Chi-restraints excluded: chain B residue 4116 SER Chi-restraints excluded: chain B residue 4144 LEU Chi-restraints excluded: chain B residue 4245 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 503 optimal weight: 5.9990 chunk 385 optimal weight: 4.9990 chunk 509 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 523 optimal weight: 4.9990 chunk 300 optimal weight: 2.9990 chunk 387 optimal weight: 0.1980 chunk 270 optimal weight: 4.9990 chunk 510 optimal weight: 0.6980 chunk 532 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3327 GLN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.097166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.082884 restraints weight = 139069.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.084628 restraints weight = 84425.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.085797 restraints weight = 59410.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.086588 restraints weight = 46478.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087037 restraints weight = 39080.134| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43944 Z= 0.114 Angle : 0.621 14.515 59704 Z= 0.297 Chirality : 0.041 0.234 6764 Planarity : 0.004 0.047 7660 Dihedral : 5.819 124.906 6020 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.85 % Allowed : 15.58 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.12), residues: 5472 helix: 1.60 (0.10), residues: 2998 sheet: -0.77 (0.24), residues: 500 loop : -1.81 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B4279 TYR 0.021 0.001 TYR A3558 PHE 0.024 0.001 PHE B2768 TRP 0.068 0.001 TRP A2502 HIS 0.012 0.001 HIS B2457 Details of bonding type rmsd covalent geometry : bond 0.00257 (43942) covalent geometry : angle 0.62079 (59704) hydrogen bonds : bond 0.03374 ( 2156) hydrogen bonds : angle 3.76510 ( 6318) Misc. bond : bond 0.00034 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 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 405 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 321 time to evaluate : 1.525 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: A 1373 GLU cc_start: 0.8412 (tt0) cc_final: 0.7787 (mm-30) REVERT: A 1397 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6608 (pp) REVERT: A 1716 ASP cc_start: 0.6263 (m-30) cc_final: 0.5018 (t0) REVERT: A 1724 MET cc_start: 0.7521 (mmp) cc_final: 0.7204 (mmp) REVERT: A 1937 ASP cc_start: 0.7404 (p0) cc_final: 0.6932 (t0) REVERT: A 1958 GLN cc_start: 0.7768 (mt0) cc_final: 0.7357 (tp-100) REVERT: A 1991 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6873 (mtp) REVERT: A 2319 SER cc_start: 0.8986 (p) cc_final: 0.8605 (m) REVERT: A 2347 ARG cc_start: 0.8052 (ttm170) cc_final: 0.7798 (ttm170) REVERT: A 2551 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8917 (tp) REVERT: A 2637 MET cc_start: 0.8571 (tpp) cc_final: 0.8309 (tpp) REVERT: A 2741 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7613 (mm) REVERT: A 2751 LEU cc_start: 0.9050 (mt) cc_final: 0.8834 (tp) REVERT: A 2822 MET cc_start: 0.8236 (ptp) cc_final: 0.7972 (ptm) REVERT: A 3336 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8103 (mt) REVERT: A 3590 ASP cc_start: 0.7663 (t0) cc_final: 0.7411 (t0) REVERT: A 3732 ASP cc_start: 0.7674 (t0) cc_final: 0.7350 (t0) REVERT: A 3810 THR cc_start: 0.8908 (m) cc_final: 0.8521 (p) REVERT: A 3911 LYS cc_start: 0.7448 (mmtt) cc_final: 0.7113 (tptp) REVERT: A 4112 GLN cc_start: 0.8129 (tt0) cc_final: 0.7761 (tm-30) REVERT: A 4296 ILE cc_start: 0.8289 (mt) cc_final: 0.7969 (mt) REVERT: B 1373 GLU cc_start: 0.8351 (tt0) cc_final: 0.7646 (mm-30) REVERT: B 1397 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6501 (pp) REVERT: B 1716 ASP cc_start: 0.6101 (m-30) cc_final: 0.5156 (t70) REVERT: B 1724 MET cc_start: 0.7532 (mmp) cc_final: 0.7236 (mmp) REVERT: B 1937 ASP cc_start: 0.7535 (p0) cc_final: 0.6838 (t0) REVERT: B 1958 GLN cc_start: 0.7700 (mt0) cc_final: 0.7463 (tp-100) REVERT: B 2319 SER cc_start: 0.8920 (p) cc_final: 0.8551 (m) REVERT: B 2741 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7698 (mm) REVERT: B 3336 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8215 (mt) REVERT: B 3810 THR cc_start: 0.8840 (m) cc_final: 0.8475 (p) REVERT: B 4112 GLN cc_start: 0.8338 (tt0) cc_final: 0.7913 (tm-30) REVERT: B 4296 ILE cc_start: 0.8335 (mt) cc_final: 0.8021 (mt) outliers start: 84 outliers final: 68 residues processed: 390 average time/residue: 0.2054 time to fit residues: 140.4152 Evaluate side-chains 386 residues out of total 4900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 310 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1394 HIS Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1747 GLU Chi-restraints excluded: chain A residue 1804 LEU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1849 PHE Chi-restraints excluded: chain A residue 1991 MET Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2352 GLU Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain A residue 2551 ILE Chi-restraints excluded: chain A residue 2564 ILE Chi-restraints excluded: chain A residue 2680 LYS Chi-restraints excluded: chain A residue 2689 GLN Chi-restraints excluded: chain A residue 2741 LEU Chi-restraints excluded: chain A residue 2884 SER Chi-restraints excluded: chain A residue 3238 PHE Chi-restraints excluded: chain A residue 3272 LEU Chi-restraints excluded: chain A residue 3308 SER Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3368 LEU Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3393 THR Chi-restraints excluded: chain A residue 3408 ILE Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3626 VAL Chi-restraints excluded: chain A residue 3688 SER Chi-restraints excluded: chain A residue 3728 SER Chi-restraints excluded: chain A residue 3766 MET Chi-restraints excluded: chain A residue 3846 SER Chi-restraints excluded: chain A residue 4116 SER Chi-restraints excluded: chain A residue 4144 LEU Chi-restraints excluded: chain A residue 4245 VAL Chi-restraints excluded: chain B residue 1374 ASP Chi-restraints excluded: chain B residue 1388 VAL Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1415 LEU Chi-restraints excluded: chain B residue 1419 LEU Chi-restraints excluded: chain B residue 1434 ASP Chi-restraints excluded: chain B residue 1533 LEU Chi-restraints excluded: chain B residue 1747 GLU Chi-restraints excluded: chain B residue 1804 LEU Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2026 THR Chi-restraints excluded: chain B residue 2064 GLU Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2106 THR Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2345 VAL Chi-restraints excluded: chain B residue 2352 GLU Chi-restraints excluded: chain B residue 2412 LEU Chi-restraints excluded: chain B residue 2427 LEU Chi-restraints excluded: chain B residue 2741 LEU Chi-restraints excluded: chain B residue 2884 SER Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain B residue 3368 LEU Chi-restraints excluded: chain B residue 3370 LEU Chi-restraints excluded: chain B residue 3393 THR Chi-restraints excluded: chain B residue 3408 ILE Chi-restraints excluded: chain B residue 3505 ILE Chi-restraints excluded: chain B residue 3626 VAL Chi-restraints excluded: chain B residue 3688 SER Chi-restraints excluded: chain B residue 3718 LEU Chi-restraints excluded: chain B residue 3728 SER Chi-restraints excluded: chain B residue 3766 MET Chi-restraints excluded: chain B residue 3846 SER Chi-restraints excluded: chain B residue 4094 LEU Chi-restraints excluded: chain B residue 4116 SER Chi-restraints excluded: chain B residue 4144 LEU Chi-restraints excluded: chain B residue 4245 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 255 optimal weight: 4.9990 chunk 365 optimal weight: 0.6980 chunk 511 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 482 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 539 optimal weight: 4.9990 chunk 464 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1614 ASN ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4017 GLN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3294 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.096537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.082510 restraints weight = 139273.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.084132 restraints weight = 86428.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.085241 restraints weight = 61913.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.085985 restraints weight = 48998.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.086493 restraints weight = 41619.396| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43944 Z= 0.121 Angle : 0.629 13.687 59704 Z= 0.301 Chirality : 0.041 0.207 6764 Planarity : 0.004 0.047 7660 Dihedral : 5.778 123.551 6020 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.85 % Allowed : 15.63 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.12), residues: 5472 helix: 1.59 (0.10), residues: 2998 sheet: -0.73 (0.24), residues: 500 loop : -1.77 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B4279 TYR 0.019 0.001 TYR A3558 PHE 0.026 0.001 PHE A2493 TRP 0.063 0.001 TRP A2502 HIS 0.008 0.001 HIS B3294 Details of bonding type rmsd covalent geometry : bond 0.00274 (43942) covalent geometry : angle 0.62938 (59704) hydrogen bonds : bond 0.03508 ( 2156) hydrogen bonds : angle 3.80729 ( 6318) Misc. bond : bond 0.00060 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6440.56 seconds wall clock time: 112 minutes 24.45 seconds (6744.45 seconds total)