Starting phenix.real_space_refine on Thu Jun 26 21:35:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pqw_17826/06_2025/8pqw_17826.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pqw_17826/06_2025/8pqw_17826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pqw_17826/06_2025/8pqw_17826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pqw_17826/06_2025/8pqw_17826.map" model { file = "/net/cci-nas-00/data/ceres_data/8pqw_17826/06_2025/8pqw_17826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pqw_17826/06_2025/8pqw_17826.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 9 5.49 5 Mg 2 5.21 5 S 151 5.16 5 C 19289 2.51 5 N 5357 2.21 5 O 5683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.61s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30491 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 22814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2892, 22814 Classifications: {'peptide': 2892} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PCIS': 4, 'PTRANS': 125, 'TRANS': 2762} Chain breaks: 13 Unresolved non-hydrogen bonds: 466 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 30, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 330 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2494 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "C" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2494 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 373 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 148 Chain: "E" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 373 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 148 Chain: "F" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 747 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'TRANS': 149} Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 365 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 8, 'GLU:plan': 30, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 316 Chain: "G" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 747 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'TRANS': 149} Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 365 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 8, 'GLU:plan': 30, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 316 Chain: "H" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 170 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 165 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'TRANS': 32} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 16.66, per 1000 atoms: 0.55 Number of scatterers: 30491 At special positions: 0 Unit cell: (166.263, 185.325, 218.154, 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 151 16.00 P 9 15.00 Mg 2 11.99 O 5683 8.00 N 5357 7.00 C 19289 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=0, symmetry=0 Time building additional restraints: 7.51 Conformation dependent library (CDL) restraints added in 4.5 seconds 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7710 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 35 sheets defined 56.5% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'A' and resid 1444 through 1472 Processing helix chain 'A' and resid 1490 through 1510 removed outlier: 3.798A pdb=" N LEU A1509 " --> pdb=" O SER A1505 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER A1510 " --> pdb=" O ALA A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1515 No H-bonds generated for 'chain 'A' and resid 1513 through 1515' Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 3.635A pdb=" N ALA A1520 " --> pdb=" O PHE A1516 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A1546 " --> pdb=" O ARG A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.835A pdb=" N SER A1585 " --> pdb=" O LYS A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1594 removed outlier: 3.672A pdb=" N ILE A1594 " --> pdb=" O ASP A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1614 Processing helix chain 'A' and resid 1615 through 1626 removed outlier: 4.030A pdb=" N LEU A1619 " --> pdb=" O LEU A1615 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A1620 " --> pdb=" O GLY A1616 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1649 through 1652 removed outlier: 3.637A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1652' Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.864A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A1658 " --> pdb=" O PHE A1654 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1653 through 1658' Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.944A pdb=" N ARG A1710 " --> pdb=" O GLU A1706 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A1729 " --> pdb=" O GLU A1725 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1766 Processing helix chain 'A' and resid 1776 through 1797 Processing helix chain 'A' and resid 1801 through 1827 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 removed outlier: 3.538A pdb=" N ALA A1898 " --> pdb=" O GLN A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1923 removed outlier: 3.554A pdb=" N VAL A1916 " --> pdb=" O LYS A1912 " (cutoff:3.500A) Processing helix chain 'A' and resid 1937 through 1952 Processing helix chain 'A' and resid 1964 through 1986 removed outlier: 3.580A pdb=" N LEU A1968 " --> pdb=" O GLU A1964 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2035 removed outlier: 3.811A pdb=" N LEU A2035 " --> pdb=" O ASN A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2058 removed outlier: 3.526A pdb=" N GLY A2058 " --> pdb=" O LEU A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.769A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2114 removed outlier: 3.782A pdb=" N SER A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A2114 " --> pdb=" O LYS A2110 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 removed outlier: 3.988A pdb=" N TRP A2234 " --> pdb=" O LYS A2230 " (cutoff:3.500A) Processing helix chain 'A' and resid 2261 through 2266 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2311 through 2315 Processing helix chain 'A' and resid 2352 through 2357 Processing helix chain 'A' and resid 2370 through 2384 removed outlier: 3.527A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2428 Proline residue: A2425 - end of helix removed outlier: 3.818A pdb=" N THR A2428 " --> pdb=" O GLN A2424 " (cutoff:3.500A) Processing helix chain 'A' and resid 2432 through 2443 removed outlier: 3.532A pdb=" N PHE A2441 " --> pdb=" O LEU A2437 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 4.013A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2504 removed outlier: 3.912A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A2495 " --> pdb=" O GLN A2491 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2548 through 2552 removed outlier: 3.503A pdb=" N VAL A2552 " --> pdb=" O TRP A2548 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2548 through 2552' Processing helix chain 'A' and resid 2571 through 2586 Processing helix chain 'A' and resid 2602 through 2610 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.355A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 removed outlier: 4.010A pdb=" N GLN A2746 " --> pdb=" O ALA A2742 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2761 through 2764 removed outlier: 4.087A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2761 through 2764' Processing helix chain 'A' and resid 2765 through 2781 removed outlier: 3.516A pdb=" N LEU A2769 " --> pdb=" O TYR A2765 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A2777 " --> pdb=" O MET A2773 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.920A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.580A pdb=" N ARG A2843 " --> pdb=" O GLU A2839 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2902 removed outlier: 3.684A pdb=" N LEU A2889 " --> pdb=" O ASP A2885 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.542A pdb=" N LEU A2916 " --> pdb=" O PHE A2912 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A2928 " --> pdb=" O ARG A2924 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 removed outlier: 3.590A pdb=" N CYS A2985 " --> pdb=" O ARG A2981 " (cutoff:3.500A) Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.666A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3047 through 3061 Processing helix chain 'A' and resid 3073 through 3082 removed outlier: 3.529A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3088 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 removed outlier: 3.857A pdb=" N ALA A3159 " --> pdb=" O HIS A3155 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A3164 " --> pdb=" O ARG A3160 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A3165 " --> pdb=" O LEU A3161 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3239 removed outlier: 3.532A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A3192 " --> pdb=" O HIS A3188 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS A3200 " --> pdb=" O GLU A3196 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A3201 " --> pdb=" O GLN A3197 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A3209 " --> pdb=" O LEU A3205 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A3221 " --> pdb=" O GLU A3217 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A3230 " --> pdb=" O SER A3226 " (cutoff:3.500A) Processing helix chain 'A' and resid 3451 through 3502 removed outlier: 3.971A pdb=" N ALA A3477 " --> pdb=" O ASN A3473 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A3478 " --> pdb=" O ARG A3474 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A3488 " --> pdb=" O ALA A3484 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS A3491 " --> pdb=" O GLU A3487 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS A3497 " --> pdb=" O SER A3493 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN A3498 " --> pdb=" O GLU A3494 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) Processing helix chain 'A' and resid 3502 through 3516 removed outlier: 3.506A pdb=" N LEU A3509 " --> pdb=" O GLY A3505 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A3516 " --> pdb=" O ALA A3512 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3548 through 3554 removed outlier: 3.820A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 removed outlier: 3.528A pdb=" N THR A3574 " --> pdb=" O ASP A3570 " (cutoff:3.500A) Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 4.089A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3619 through 3630 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3696 removed outlier: 3.850A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A3696 " --> pdb=" O LEU A3692 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3755 removed outlier: 3.800A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3764 through 3818 removed outlier: 4.137A pdb=" N VAL A3784 " --> pdb=" O VAL A3780 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU A3785 " --> pdb=" O THR A3781 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A3786 " --> pdb=" O ARG A3782 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.719A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR A3841 " --> pdb=" O HIS A3837 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.901A pdb=" N SER A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3895 removed outlier: 4.102A pdb=" N PHE A3883 " --> pdb=" O ASP A3879 " (cutoff:3.500A) Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 removed outlier: 3.633A pdb=" N GLN A3952 " --> pdb=" O ILE A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3996 Processing helix chain 'A' and resid 3997 through 3999 No H-bonds generated for 'chain 'A' and resid 3997 through 3999' Processing helix chain 'A' and resid 4000 through 4013 Processing helix chain 'A' and resid 4026 through 4034 removed outlier: 3.844A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 Processing helix chain 'A' and resid 4073 through 4090 Processing helix chain 'A' and resid 4098 through 4101 removed outlier: 3.735A pdb=" N LEU A4101 " --> pdb=" O ASN A4098 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4098 through 4101' Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 4.115A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 removed outlier: 3.509A pdb=" N GLY A4142 " --> pdb=" O LEU A4138 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.925A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4193 Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.855A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 removed outlier: 3.524A pdb=" N LEU A4243 " --> pdb=" O PRO A4239 " (cutoff:3.500A) Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 removed outlier: 3.745A pdb=" N PHE A4278 " --> pdb=" O THR A4274 " (cutoff:3.500A) Processing helix chain 'A' and resid 4301 through 4310 removed outlier: 3.580A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4328 through 4348 removed outlier: 3.755A pdb=" N MET A4348 " --> pdb=" O LEU A4344 " (cutoff:3.500A) Processing helix chain 'A' and resid 4380 through 4391 Processing helix chain 'A' and resid 4392 through 4395 Processing helix chain 'A' and resid 4407 through 4439 removed outlier: 3.707A pdb=" N ARG A4411 " --> pdb=" O ASP A4407 " (cutoff:3.500A) Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4498 removed outlier: 3.671A pdb=" N SER A4480 " --> pdb=" O ILE A4476 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A4498 " --> pdb=" O LEU A4494 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.563A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4631 through 4638 Processing helix chain 'B' and resid 286 through 297 removed outlier: 4.063A pdb=" N SER B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 294 " --> pdb=" O TYR B 290 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 297 removed outlier: 3.818A pdb=" N SER C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 22 Processing helix chain 'D' and resid 24 through 35 removed outlier: 3.521A pdb=" N ALA D 35 " --> pdb=" O PHE D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 47 removed outlier: 3.515A pdb=" N TYR D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 75 removed outlier: 3.558A pdb=" N LEU D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER D 70 " --> pdb=" O MET D 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 22 Processing helix chain 'E' and resid 24 through 35 Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.578A pdb=" N LYS E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 49 through 57 Processing helix chain 'E' and resid 57 through 75 removed outlier: 4.142A pdb=" N MET E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 437 removed outlier: 3.679A pdb=" N GLU F 403 " --> pdb=" O ASN F 399 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL F 405 " --> pdb=" O GLU F 401 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 468 removed outlier: 4.413A pdb=" N MET F 442 " --> pdb=" O GLU F 438 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL F 454 " --> pdb=" O LEU F 450 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG F 455 " --> pdb=" O GLU F 451 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA F 466 " --> pdb=" O GLY F 462 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET F 467 " --> pdb=" O ASP F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 541 removed outlier: 3.502A pdb=" N ARG F 502 " --> pdb=" O GLU F 498 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN F 515 " --> pdb=" O ALA F 511 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN F 522 " --> pdb=" O LYS F 518 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN F 536 " --> pdb=" O ARG F 532 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN F 537 " --> pdb=" O GLU F 533 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU F 539 " --> pdb=" O THR F 535 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA F 540 " --> pdb=" O ASN F 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 434 removed outlier: 4.266A pdb=" N GLU G 428 " --> pdb=" O ASP G 424 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN G 429 " --> pdb=" O GLU G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 543 removed outlier: 3.777A pdb=" N ALA G 466 " --> pdb=" O GLY G 462 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU G 504 " --> pdb=" O GLN G 500 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA G 505 " --> pdb=" O LYS G 501 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA G 506 " --> pdb=" O ARG G 502 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU G 539 " --> pdb=" O THR G 535 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA G 540 " --> pdb=" O ASN G 536 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU G 543 " --> pdb=" O GLU G 539 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 35 removed outlier: 3.653A pdb=" N LYS H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 34 removed outlier: 5.372A pdb=" N GLU I 29 " --> pdb=" O LYS I 25 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU I 30 " --> pdb=" O LYS I 26 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.374A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 3.676A pdb=" N GLY A1675 " --> pdb=" O ILE A1665 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 6.482A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE A1930 " --> pdb=" O ASP A1958 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR A2017 " --> pdb=" O GLY A1955 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE A1957 " --> pdb=" O THR A2017 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 removed outlier: 3.849A pdb=" N CYS A1999 " --> pdb=" O VAL A2006 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A2006 " --> pdb=" O CYS A1999 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2254 Processing sheet with id=AA8, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AA9, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.428A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A2591 " --> pdb=" O PHE A2708 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL A2592 " --> pdb=" O VAL A2734 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 6.570A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2873 through 2874 Processing sheet with id=AB3, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.401A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A3067 " --> pdb=" O MET A2994 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.219A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR A3681 " --> pdb=" O PRO A3587 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A3589 " --> pdb=" O THR A3681 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB6, first strand: chain 'A' and resid 4068 through 4070 removed outlier: 6.864A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 6.717A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.094A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4563 through 4564 removed outlier: 4.166A pdb=" N LEU A4563 " --> pdb=" O LEU A4585 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.922A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AC3, first strand: chain 'B' and resid 95 through 96 removed outlier: 4.568A pdb=" N THR B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 399 " --> pdb=" O THR B 403 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 111 through 116 removed outlier: 6.424A pdb=" N ILE B 132 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR B 145 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 134 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 153 through 158 removed outlier: 3.748A pdb=" N ASP B 155 " --> pdb=" O CYS B 168 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 169 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N THR B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE B 174 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR B 187 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 176 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 206 through 210 removed outlier: 6.860A pdb=" N GLU B 220 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS B 226 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 237 through 242 removed outlier: 3.608A pdb=" N MET B 239 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 270 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL B 262 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N CYS B 268 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 279 through 284 removed outlier: 3.581A pdb=" N SER B 315 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N THR B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE B 320 " --> pdb=" O THR B 333 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR B 333 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET B 322 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP B 324 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET B 329 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 341 through 346 removed outlier: 3.759A pdb=" N THR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS B 374 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP B 366 " --> pdb=" O CYS B 372 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N CYS B 372 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 95 through 96 Processing sheet with id=AD2, first strand: chain 'C' and resid 95 through 96 removed outlier: 4.551A pdb=" N THR C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 399 " --> pdb=" O THR C 403 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 111 through 116 removed outlier: 5.687A pdb=" N ASP C 136 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHE C 142 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 155 through 158 removed outlier: 4.144A pdb=" N ASP C 155 " --> pdb=" O CYS C 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS C 168 " --> pdb=" O ASP C 155 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP C 178 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS C 184 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 195 through 200 removed outlier: 3.673A pdb=" N SER C 211 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU C 220 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS C 226 " --> pdb=" O GLU C 220 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 237 through 242 removed outlier: 6.590A pdb=" N VAL C 262 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS C 268 " --> pdb=" O VAL C 262 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 279 through 284 removed outlier: 4.494A pdb=" N THR C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE C 320 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR C 333 " --> pdb=" O ILE C 320 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET C 322 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 341 through 346 removed outlier: 3.734A pdb=" N ALA C 357 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP C 366 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N CYS C 372 " --> pdb=" O ASP C 366 " (cutoff:3.500A) 1861 hydrogen bonds defined for protein. 5463 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: 23.20 Time building geometry restraints manager: 8.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10052 1.34 - 1.46: 6846 1.46 - 1.58: 13941 1.58 - 1.71: 11 1.71 - 1.83: 245 Bond restraints: 31095 Sorted by residual: bond pdb=" CA GLU A1610 " pdb=" C GLU A1610 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.24e-02 6.50e+03 6.57e+00 bond pdb=" CA GLU A1567 " pdb=" C GLU A1567 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.27e-02 6.20e+03 4.11e+00 bond pdb=" C GLU A2767 " pdb=" N PRO A2768 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.38e+00 bond pdb=" N ASN A2860 " pdb=" CA ASN A2860 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.24e+00 bond pdb=" CB CYS A1932 " pdb=" SG CYS A1932 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 2.98e+00 ... (remaining 31090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 41633 2.84 - 5.68: 569 5.68 - 8.52: 83 8.52 - 11.37: 17 11.37 - 14.21: 8 Bond angle restraints: 42310 Sorted by residual: angle pdb=" N GLU H 12 " pdb=" CA GLU H 12 " pdb=" CB GLU H 12 " ideal model delta sigma weight residual 110.16 117.58 -7.42 1.48e+00 4.57e-01 2.51e+01 angle pdb=" CB MET A1685 " pdb=" CG MET A1685 " pdb=" SD MET A1685 " ideal model delta sigma weight residual 112.70 126.91 -14.21 3.00e+00 1.11e-01 2.24e+01 angle pdb=" N LEU A2668 " pdb=" CA LEU A2668 " pdb=" C LEU A2668 " ideal model delta sigma weight residual 109.81 119.83 -10.02 2.21e+00 2.05e-01 2.06e+01 angle pdb=" CB MET A3008 " pdb=" CG MET A3008 " pdb=" SD MET A3008 " ideal model delta sigma weight residual 112.70 126.20 -13.50 3.00e+00 1.11e-01 2.03e+01 angle pdb=" CA LYS A4133 " pdb=" CB LYS A4133 " pdb=" CG LYS A4133 " ideal model delta sigma weight residual 114.10 122.78 -8.68 2.00e+00 2.50e-01 1.88e+01 ... (remaining 42305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.59: 18161 31.59 - 63.17: 489 63.17 - 94.76: 45 94.76 - 126.35: 2 126.35 - 157.93: 1 Dihedral angle restraints: 18698 sinusoidal: 6889 harmonic: 11809 Sorted by residual: dihedral pdb=" O2A ADP A4806 " pdb=" O3A ADP A4806 " pdb=" PA ADP A4806 " pdb=" PB ADP A4806 " ideal model delta sinusoidal sigma weight residual -60.00 97.93 -157.93 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C5' ADP A4806 " pdb=" O5' ADP A4806 " pdb=" PA ADP A4806 " pdb=" O2A ADP A4806 " ideal model delta sinusoidal sigma weight residual -60.00 61.26 -121.26 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" CA PRO A2812 " pdb=" C PRO A2812 " pdb=" N LEU A2813 " pdb=" CA LEU A2813 " ideal model delta harmonic sigma weight residual -180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 18695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3978 0.062 - 0.124: 795 0.124 - 0.185: 113 0.185 - 0.247: 16 0.247 - 0.309: 3 Chirality restraints: 4905 Sorted by residual: chirality pdb=" CG LEU A3745 " pdb=" CB LEU A3745 " pdb=" CD1 LEU A3745 " pdb=" CD2 LEU A3745 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB ILE A3924 " pdb=" CA ILE A3924 " pdb=" CG1 ILE A3924 " pdb=" CG2 ILE A3924 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB VAL A3638 " pdb=" CA VAL A3638 " pdb=" CG1 VAL A3638 " pdb=" CG2 VAL A3638 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 4902 not shown) Planarity restraints: 5441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1936 " -0.027 2.00e-02 2.50e+03 3.37e-02 1.99e+01 pdb=" CG PHE A1936 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A1936 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE A1936 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A1936 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A1936 " -0.027 2.00e-02 2.50e+03 pdb=" CZ PHE A1936 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A2811 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO A2812 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A2812 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A2812 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2795 " 0.044 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO A2796 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A2796 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A2796 " 0.037 5.00e-02 4.00e+02 ... (remaining 5438 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 115 2.45 - 3.07: 18139 3.07 - 3.68: 49382 3.68 - 4.29: 68826 4.29 - 4.90: 111494 Nonbonded interactions: 247956 Sorted by model distance: nonbonded pdb=" O2B ADP A4801 " pdb="MG MG A4802 " model vdw 1.844 2.170 nonbonded pdb=" OE2 GLU A2344 " pdb=" O1G ATP A4803 " model vdw 1.964 3.040 nonbonded pdb=" OD2 ASP A1958 " pdb="MG MG A4802 " model vdw 2.032 2.170 nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4804 " model vdw 2.189 2.170 nonbonded pdb=" OH TYR A4180 " pdb=" OD1 ASP A4220 " model vdw 2.240 3.040 ... (remaining 247951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and resid 3 through 35) selection = chain 'I' } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.260 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 79.770 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31095 Z= 0.201 Angle : 0.861 14.207 42310 Z= 0.448 Chirality : 0.051 0.309 4905 Planarity : 0.006 0.077 5441 Dihedral : 14.739 157.932 10988 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.03 % Allowed : 0.36 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.12), residues: 3987 helix: -0.96 (0.10), residues: 2089 sheet: -0.78 (0.23), residues: 489 loop : -1.14 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 135 HIS 0.019 0.001 HIS C 193 PHE 0.069 0.002 PHE A1936 TYR 0.030 0.002 TYR A3836 ARG 0.012 0.001 ARG A2811 Details of bonding type rmsd hydrogen bonds : bond 0.15647 ( 1857) hydrogen bonds : angle 6.73340 ( 5463) covalent geometry : bond 0.00416 (31095) covalent geometry : angle 0.86077 (42310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 3.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2012 MET cc_start: 0.7762 (mmm) cc_final: 0.7497 (mmm) REVERT: A 2493 TYR cc_start: 0.7934 (t80) cc_final: 0.7565 (t80) REVERT: A 3030 MET cc_start: 0.8628 (mpp) cc_final: 0.7675 (mpp) REVERT: A 4004 MET cc_start: 0.7082 (mmp) cc_final: 0.6775 (mmp) REVERT: B 188 MET cc_start: 0.7731 (mmm) cc_final: 0.7487 (mmm) REVERT: C 188 MET cc_start: 0.8417 (mpp) cc_final: 0.8185 (mpp) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.4031 time to fit residues: 110.8008 Evaluate side-chains 133 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 338 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 314 optimal weight: 30.0000 chunk 121 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 233 optimal weight: 5.9990 chunk 364 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1855 GLN A1867 ASN ** A2109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** A3009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3869 ASN ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4108 GLN ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4466 HIS B 154 GLN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.038450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.032499 restraints weight = 365416.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.033347 restraints weight = 210936.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.033579 restraints weight = 117224.140| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31095 Z= 0.227 Angle : 0.645 9.011 42310 Z= 0.336 Chirality : 0.041 0.151 4905 Planarity : 0.005 0.058 5441 Dihedral : 6.972 159.234 4366 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.13), residues: 3987 helix: 0.64 (0.11), residues: 2143 sheet: -0.60 (0.24), residues: 462 loop : -0.95 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 177 HIS 0.005 0.001 HIS A4006 PHE 0.027 0.002 PHE A1936 TYR 0.017 0.002 TYR A3552 ARG 0.006 0.001 ARG A2358 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 1857) hydrogen bonds : angle 4.61085 ( 5463) covalent geometry : bond 0.00480 (31095) covalent geometry : angle 0.64457 (42310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 4.034 Fit side-chains REVERT: A 3008 MET cc_start: 0.9344 (mmm) cc_final: 0.9134 (tpp) REVERT: A 3030 MET cc_start: 0.8614 (mpp) cc_final: 0.8096 (mpp) REVERT: A 3791 MET cc_start: 0.9008 (ppp) cc_final: 0.8720 (ppp) REVERT: B 188 MET cc_start: 0.8422 (mmm) cc_final: 0.7846 (mmm) REVERT: C 188 MET cc_start: 0.8222 (mpp) cc_final: 0.8015 (mpp) outliers start: 1 outliers final: 1 residues processed: 153 average time/residue: 0.4243 time to fit residues: 116.5585 Evaluate side-chains 131 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 17 optimal weight: 9.9990 chunk 226 optimal weight: 0.0870 chunk 291 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 48 optimal weight: 20.0000 chunk 392 optimal weight: 5.9990 chunk 247 optimal weight: 5.9990 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN A2960 GLN A2998 ASN ** A3139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3156 GLN ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4012 ASN ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.038679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.032792 restraints weight = 370893.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.033635 restraints weight = 214556.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.033847 restraints weight = 123202.514| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31095 Z= 0.172 Angle : 0.582 8.607 42310 Z= 0.300 Chirality : 0.040 0.171 4905 Planarity : 0.004 0.077 5441 Dihedral : 6.689 157.181 4366 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.13), residues: 3987 helix: 1.39 (0.11), residues: 2152 sheet: -0.57 (0.23), residues: 471 loop : -0.82 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A3097 HIS 0.004 0.001 HIS B 233 PHE 0.022 0.002 PHE A1936 TYR 0.016 0.002 TYR A3836 ARG 0.007 0.000 ARG A2492 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 1857) hydrogen bonds : angle 4.27597 ( 5463) covalent geometry : bond 0.00368 (31095) covalent geometry : angle 0.58186 (42310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 3.573 Fit side-chains revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8248 (tmm) cc_final: 0.7931 (tmm) REVERT: A 1967 MET cc_start: 0.8783 (tpp) cc_final: 0.8501 (mmm) REVERT: A 2012 MET cc_start: 0.8172 (mmm) cc_final: 0.7377 (mmm) REVERT: A 2777 TYR cc_start: 0.8795 (t80) cc_final: 0.7316 (t80) REVERT: A 2799 MET cc_start: 0.8795 (mpp) cc_final: 0.8016 (mpp) REVERT: A 3008 MET cc_start: 0.9351 (mmm) cc_final: 0.9075 (tpp) REVERT: A 3030 MET cc_start: 0.8728 (mpp) cc_final: 0.8151 (mpp) REVERT: A 3524 MET cc_start: 0.7822 (tpp) cc_final: 0.7553 (tpp) REVERT: A 3791 MET cc_start: 0.8979 (ppp) cc_final: 0.8698 (ppp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3948 time to fit residues: 111.5871 Evaluate side-chains 131 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 358 optimal weight: 0.0060 chunk 108 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 313 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 385 optimal weight: 30.0000 chunk 206 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3139 HIS ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3907 HIS ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 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 = 0.3320 r_free = 0.3320 target = 0.038686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.032714 restraints weight = 371620.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.033583 restraints weight = 212739.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.033754 restraints weight = 123157.473| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31095 Z= 0.151 Angle : 0.559 9.232 42310 Z= 0.286 Chirality : 0.040 0.209 4905 Planarity : 0.004 0.054 5441 Dihedral : 6.511 155.448 4366 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3987 helix: 1.72 (0.11), residues: 2169 sheet: -0.56 (0.23), residues: 493 loop : -0.80 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 261 HIS 0.003 0.001 HIS B 233 PHE 0.014 0.001 PHE A1936 TYR 0.016 0.001 TYR A3836 ARG 0.004 0.000 ARG C 316 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 1857) hydrogen bonds : angle 4.09227 ( 5463) covalent geometry : bond 0.00325 (31095) covalent geometry : angle 0.55867 (42310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 3.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8278 (tmm) cc_final: 0.7979 (tmm) REVERT: A 1709 MET cc_start: 0.8909 (ptp) cc_final: 0.8708 (ptp) REVERT: A 2012 MET cc_start: 0.8084 (mmm) cc_final: 0.7237 (mmm) REVERT: A 2461 MET cc_start: 0.8333 (mmp) cc_final: 0.8089 (mmp) REVERT: A 2776 PHE cc_start: 0.8520 (t80) cc_final: 0.8288 (t80) REVERT: A 2777 TYR cc_start: 0.8795 (t80) cc_final: 0.7401 (t80) REVERT: A 3008 MET cc_start: 0.9339 (mmm) cc_final: 0.9087 (tpp) REVERT: A 3030 MET cc_start: 0.8577 (mpp) cc_final: 0.8191 (mpp) REVERT: A 3068 MET cc_start: 0.8689 (ptp) cc_final: 0.8322 (ptp) REVERT: A 3500 MET cc_start: 0.7673 (tmm) cc_final: 0.7305 (tmm) REVERT: A 3524 MET cc_start: 0.7868 (tpp) cc_final: 0.7566 (tpp) REVERT: A 3791 MET cc_start: 0.8973 (ppp) cc_final: 0.8710 (ppp) REVERT: B 188 MET cc_start: 0.8267 (mmm) cc_final: 0.7705 (mmm) REVERT: B 239 MET cc_start: 0.5428 (tmm) cc_final: 0.5193 (tmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.4085 time to fit residues: 114.3977 Evaluate side-chains 132 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 258 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 361 optimal weight: 40.0000 chunk 208 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 382 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 309 optimal weight: 9.9990 chunk 42 optimal weight: 30.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1646 ASN A1863 ASN A1894 GLN A2377 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A2964 HIS ** A3156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3622 ASN ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.037887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.032028 restraints weight = 377320.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.032859 restraints weight = 223331.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.033039 restraints weight = 121025.419| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 31095 Z= 0.239 Angle : 0.659 9.937 42310 Z= 0.338 Chirality : 0.042 0.189 4905 Planarity : 0.004 0.056 5441 Dihedral : 6.676 156.120 4366 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.13), residues: 3987 helix: 1.55 (0.11), residues: 2179 sheet: -0.72 (0.23), residues: 513 loop : -0.96 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 323 HIS 0.005 0.001 HIS B 233 PHE 0.026 0.002 PHE A2682 TYR 0.016 0.002 TYR A3552 ARG 0.006 0.001 ARG A1943 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 1857) hydrogen bonds : angle 4.30232 ( 5463) covalent geometry : bond 0.00518 (31095) covalent geometry : angle 0.65853 (42310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 3.510 Fit side-chains revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8105 (tmm) cc_final: 0.7895 (tmm) REVERT: A 2012 MET cc_start: 0.8299 (mmm) cc_final: 0.7611 (mmm) REVERT: A 2755 MET cc_start: 0.7988 (ptm) cc_final: 0.7709 (ptm) REVERT: A 2777 TYR cc_start: 0.8861 (t80) cc_final: 0.7826 (t80) REVERT: A 3008 MET cc_start: 0.9352 (mmm) cc_final: 0.9078 (tpp) REVERT: A 3030 MET cc_start: 0.8721 (mpp) cc_final: 0.8152 (mpp) REVERT: A 3068 MET cc_start: 0.8731 (ptp) cc_final: 0.8451 (ptp) REVERT: A 3126 MET cc_start: 0.8194 (tpt) cc_final: 0.7851 (tpt) REVERT: A 3524 MET cc_start: 0.7952 (tpp) cc_final: 0.7691 (tpp) REVERT: A 3791 MET cc_start: 0.9004 (ppp) cc_final: 0.8735 (ppp) REVERT: A 4339 MET cc_start: 0.8549 (ppp) cc_final: 0.8317 (ppp) REVERT: B 188 MET cc_start: 0.8469 (mmm) cc_final: 0.7747 (mmm) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.3954 time to fit residues: 105.0853 Evaluate side-chains 131 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 307 optimal weight: 50.0000 chunk 309 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 351 optimal weight: 7.9990 chunk 241 optimal weight: 3.9990 chunk 396 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 0.0000 chunk 283 optimal weight: 20.0000 chunk 227 optimal weight: 0.0050 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1646 ASN A1894 GLN A2377 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2998 ASN A3139 HIS A3156 GLN ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3907 HIS A4131 ASN ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.038415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.032548 restraints weight = 372908.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.033257 restraints weight = 212382.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.033484 restraints weight = 123976.072| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31095 Z= 0.149 Angle : 0.576 9.745 42310 Z= 0.293 Chirality : 0.041 0.166 4905 Planarity : 0.004 0.056 5441 Dihedral : 6.513 154.847 4366 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3987 helix: 1.83 (0.11), residues: 2180 sheet: -0.68 (0.23), residues: 507 loop : -0.88 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1741 HIS 0.005 0.001 HIS A3139 PHE 0.015 0.001 PHE A2343 TYR 0.013 0.001 TYR A3827 ARG 0.006 0.000 ARG A2729 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 1857) hydrogen bonds : angle 4.09347 ( 5463) covalent geometry : bond 0.00325 (31095) covalent geometry : angle 0.57558 (42310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 3.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8131 (tmm) cc_final: 0.7902 (tmm) REVERT: A 2012 MET cc_start: 0.8179 (mmm) cc_final: 0.7358 (mmm) REVERT: A 2461 MET cc_start: 0.8343 (mmp) cc_final: 0.7991 (mmp) REVERT: A 2777 TYR cc_start: 0.8818 (t80) cc_final: 0.7812 (t80) REVERT: A 3008 MET cc_start: 0.9370 (mmm) cc_final: 0.9076 (tpp) REVERT: A 3030 MET cc_start: 0.8468 (mpp) cc_final: 0.8013 (mpp) REVERT: A 3126 MET cc_start: 0.8198 (tpt) cc_final: 0.7887 (tpt) REVERT: A 3500 MET cc_start: 0.7734 (tmm) cc_final: 0.7312 (tmm) REVERT: A 3524 MET cc_start: 0.7929 (tpp) cc_final: 0.7652 (tpp) REVERT: A 3791 MET cc_start: 0.8939 (ppp) cc_final: 0.8674 (ppp) REVERT: A 4043 MET cc_start: 0.7269 (tpt) cc_final: 0.6898 (tpt) REVERT: B 188 MET cc_start: 0.8463 (mmm) cc_final: 0.7830 (mmm) REVERT: B 239 MET cc_start: 0.5048 (tmm) cc_final: 0.4821 (tmm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.3971 time to fit residues: 105.9778 Evaluate side-chains 129 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 96 optimal weight: 4.9990 chunk 265 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 273 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 278 optimal weight: 6.9990 chunk 366 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 chunk 243 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1646 ASN A2377 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2998 ASN ** A3156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4335 GLN ** 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 = 0.3299 r_free = 0.3299 target = 0.038165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.032233 restraints weight = 373914.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.033077 restraints weight = 219440.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.033311 restraints weight = 121059.932| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31095 Z= 0.186 Angle : 0.608 9.722 42310 Z= 0.310 Chirality : 0.041 0.168 4905 Planarity : 0.004 0.056 5441 Dihedral : 6.470 154.375 4366 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3987 helix: 1.85 (0.11), residues: 2165 sheet: -0.68 (0.23), residues: 501 loop : -0.85 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 236 HIS 0.004 0.001 HIS B 233 PHE 0.016 0.002 PHE A2682 TYR 0.012 0.001 TYR A3552 ARG 0.008 0.000 ARG C 238 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 1857) hydrogen bonds : angle 4.13988 ( 5463) covalent geometry : bond 0.00403 (31095) covalent geometry : angle 0.60788 (42310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8137 (tmm) cc_final: 0.7922 (tmm) REVERT: A 1709 MET cc_start: 0.9045 (ptp) cc_final: 0.8801 (ptp) REVERT: A 2012 MET cc_start: 0.8190 (mmm) cc_final: 0.7553 (mmm) REVERT: A 3008 MET cc_start: 0.9393 (mmm) cc_final: 0.9138 (tpp) REVERT: A 3030 MET cc_start: 0.8488 (mpp) cc_final: 0.8153 (mpp) REVERT: A 3068 MET cc_start: 0.8759 (ptp) cc_final: 0.8400 (ptp) REVERT: A 3126 MET cc_start: 0.8260 (tpt) cc_final: 0.7975 (tpt) REVERT: A 3524 MET cc_start: 0.7992 (tpp) cc_final: 0.7692 (tpp) REVERT: A 3791 MET cc_start: 0.8940 (ppp) cc_final: 0.8670 (ppp) REVERT: A 4339 MET cc_start: 0.8678 (ppp) cc_final: 0.8353 (ppp) REVERT: B 188 MET cc_start: 0.8485 (mmm) cc_final: 0.7829 (mmm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.4196 time to fit residues: 110.0424 Evaluate side-chains 130 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 267 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 323 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 186 optimal weight: 0.0270 chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 394 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 327 optimal weight: 5.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2377 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2998 ASN B 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.038505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.032656 restraints weight = 372006.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.033405 restraints weight = 216034.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.033639 restraints weight = 126243.262| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31095 Z= 0.140 Angle : 0.567 10.746 42310 Z= 0.288 Chirality : 0.041 0.179 4905 Planarity : 0.004 0.055 5441 Dihedral : 6.320 153.208 4366 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.14), residues: 3987 helix: 2.02 (0.11), residues: 2181 sheet: -0.58 (0.23), residues: 497 loop : -0.83 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 236 HIS 0.004 0.001 HIS A3151 PHE 0.036 0.001 PHE A2682 TYR 0.012 0.001 TYR A2693 ARG 0.007 0.000 ARG A2643 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 1857) hydrogen bonds : angle 3.99156 ( 5463) covalent geometry : bond 0.00305 (31095) covalent geometry : angle 0.56714 (42310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8104 (tmm) cc_final: 0.7877 (tmm) REVERT: A 2012 MET cc_start: 0.8145 (mmm) cc_final: 0.7446 (mmm) REVERT: A 2777 TYR cc_start: 0.8789 (t80) cc_final: 0.7613 (t80) REVERT: A 2799 MET cc_start: 0.8602 (mpp) cc_final: 0.7954 (mpp) REVERT: A 3008 MET cc_start: 0.9358 (mmm) cc_final: 0.9075 (tpp) REVERT: A 3030 MET cc_start: 0.8536 (mpp) cc_final: 0.8127 (mpp) REVERT: A 3068 MET cc_start: 0.8680 (ptp) cc_final: 0.8326 (ptp) REVERT: A 3126 MET cc_start: 0.8276 (tpt) cc_final: 0.7982 (tpt) REVERT: A 3500 MET cc_start: 0.7763 (tmm) cc_final: 0.7062 (tmm) REVERT: A 3524 MET cc_start: 0.7945 (tpp) cc_final: 0.7632 (tpp) REVERT: A 3791 MET cc_start: 0.8918 (ppp) cc_final: 0.8639 (ppp) REVERT: A 4043 MET cc_start: 0.7073 (tpt) cc_final: 0.6679 (tpt) REVERT: C 123 MET cc_start: 0.8813 (ppp) cc_final: 0.8278 (ppp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.3981 time to fit residues: 107.2616 Evaluate side-chains 129 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 290 optimal weight: 0.2980 chunk 268 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 289 optimal weight: 0.8980 chunk 199 optimal weight: 0.0970 chunk 238 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 297 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2047 GLN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.039323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.033373 restraints weight = 366191.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.034208 restraints weight = 217628.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.034458 restraints weight = 125733.998| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 31095 Z= 0.103 Angle : 0.539 9.313 42310 Z= 0.272 Chirality : 0.040 0.169 4905 Planarity : 0.004 0.054 5441 Dihedral : 6.097 150.358 4366 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.14), residues: 3987 helix: 2.30 (0.11), residues: 2173 sheet: -0.47 (0.23), residues: 492 loop : -0.72 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 236 HIS 0.008 0.001 HIS A4389 PHE 0.035 0.001 PHE A2682 TYR 0.016 0.001 TYR A4049 ARG 0.006 0.000 ARG A2643 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 1857) hydrogen bonds : angle 3.78163 ( 5463) covalent geometry : bond 0.00210 (31095) covalent geometry : angle 0.53868 (42310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 4.059 Fit side-chains revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8043 (tmm) cc_final: 0.7816 (tmm) REVERT: A 1685 MET cc_start: 0.8346 (mmm) cc_final: 0.7955 (mmm) REVERT: A 2012 MET cc_start: 0.8163 (mmm) cc_final: 0.7328 (mmm) REVERT: A 2461 MET cc_start: 0.8234 (mmp) cc_final: 0.7948 (mmp) REVERT: A 2777 TYR cc_start: 0.8691 (t80) cc_final: 0.7612 (t80) REVERT: A 2799 MET cc_start: 0.8445 (mpp) cc_final: 0.7905 (mpp) REVERT: A 3008 MET cc_start: 0.9255 (mmm) cc_final: 0.9044 (tpp) REVERT: A 3030 MET cc_start: 0.8574 (mpp) cc_final: 0.8115 (mpp) REVERT: A 3068 MET cc_start: 0.8596 (ptp) cc_final: 0.8289 (ptp) REVERT: A 3126 MET cc_start: 0.8162 (tpt) cc_final: 0.7863 (tpt) REVERT: A 3500 MET cc_start: 0.7860 (tmm) cc_final: 0.7236 (tmm) REVERT: A 3524 MET cc_start: 0.7829 (tpp) cc_final: 0.7601 (tpp) REVERT: A 3791 MET cc_start: 0.8962 (ppp) cc_final: 0.8711 (ppp) REVERT: A 4128 MET cc_start: 0.7672 (pmm) cc_final: 0.6463 (pmm) REVERT: A 4339 MET cc_start: 0.8646 (ppp) cc_final: 0.8342 (ppp) REVERT: B 188 MET cc_start: 0.7987 (mmm) cc_final: 0.7543 (mmt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.4339 time to fit residues: 123.4452 Evaluate side-chains 132 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 269 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 377 optimal weight: 30.0000 chunk 247 optimal weight: 8.9990 chunk 219 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1855 GLN A2377 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4012 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.038133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.032316 restraints weight = 374712.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.033091 restraints weight = 226035.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.033290 restraints weight = 129476.160| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31095 Z= 0.196 Angle : 0.616 9.777 42310 Z= 0.314 Chirality : 0.041 0.165 4905 Planarity : 0.004 0.060 5441 Dihedral : 6.249 151.576 4366 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.14), residues: 3987 helix: 2.09 (0.11), residues: 2177 sheet: -0.60 (0.23), residues: 501 loop : -0.78 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 236 HIS 0.007 0.001 HIS C 193 PHE 0.033 0.002 PHE A1936 TYR 0.015 0.002 TYR A3552 ARG 0.010 0.001 ARG A2684 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 1857) hydrogen bonds : angle 4.00149 ( 5463) covalent geometry : bond 0.00423 (31095) covalent geometry : angle 0.61569 (42310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 3.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2012 MET cc_start: 0.8179 (mmm) cc_final: 0.7527 (mmm) REVERT: A 2461 MET cc_start: 0.8303 (mmp) cc_final: 0.8014 (mmp) REVERT: A 2777 TYR cc_start: 0.8777 (t80) cc_final: 0.7609 (t80) REVERT: A 2799 MET cc_start: 0.8615 (mpp) cc_final: 0.8000 (mpp) REVERT: A 3008 MET cc_start: 0.9346 (mmm) cc_final: 0.9088 (tpp) REVERT: A 3030 MET cc_start: 0.8458 (mpp) cc_final: 0.8023 (mpp) REVERT: A 3068 MET cc_start: 0.8694 (ptp) cc_final: 0.8385 (ptp) REVERT: A 3126 MET cc_start: 0.8340 (tpt) cc_final: 0.8074 (tpt) REVERT: A 3500 MET cc_start: 0.7774 (tmm) cc_final: 0.7045 (tmm) REVERT: A 3524 MET cc_start: 0.7946 (tpp) cc_final: 0.7707 (tpp) REVERT: A 3791 MET cc_start: 0.8960 (ppp) cc_final: 0.8701 (ppp) REVERT: A 4128 MET cc_start: 0.7809 (pmm) cc_final: 0.6671 (pmm) REVERT: B 188 MET cc_start: 0.8128 (mmm) cc_final: 0.7649 (mmm) REVERT: C 239 MET cc_start: 0.7628 (tmm) cc_final: 0.7427 (tmm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.4005 time to fit residues: 106.2648 Evaluate side-chains 130 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 301 optimal weight: 20.0000 chunk 340 optimal weight: 7.9990 chunk 338 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 303 optimal weight: 30.0000 chunk 157 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2377 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2998 ASN ** A3156 GLN ** 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 = 0.3299 r_free = 0.3299 target = 0.038126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.032310 restraints weight = 375666.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.033023 restraints weight = 221789.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.033196 restraints weight = 145481.298| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31095 Z= 0.194 Angle : 0.615 9.898 42310 Z= 0.313 Chirality : 0.042 0.175 4905 Planarity : 0.004 0.055 5441 Dihedral : 6.344 152.753 4366 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3987 helix: 1.99 (0.11), residues: 2181 sheet: -0.67 (0.23), residues: 491 loop : -0.84 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 236 HIS 0.019 0.001 HIS C 277 PHE 0.035 0.002 PHE A1936 TYR 0.014 0.001 TYR A3836 ARG 0.011 0.000 ARG C 316 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 1857) hydrogen bonds : angle 4.05929 ( 5463) covalent geometry : bond 0.00421 (31095) covalent geometry : angle 0.61468 (42310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9957.18 seconds wall clock time: 174 minutes 49.46 seconds (10489.46 seconds total)