Starting phenix.real_space_refine on Fri Jul 26 01:42:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqw_17826/07_2024/8pqw_17826_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqw_17826/07_2024/8pqw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqw_17826/07_2024/8pqw_17826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqw_17826/07_2024/8pqw_17826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqw_17826/07_2024/8pqw_17826_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqw_17826/07_2024/8pqw_17826_neut.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 Residue "A PHE 1534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1567": "OE1" <-> "OE2" Residue "A GLU 1610": "OE1" <-> "OE2" Residue "A PHE 1957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2195": "OD1" <-> "OD2" Residue "A TYR 2493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2808": "OE1" <-> "OE2" Residue "A ASP 2880": "OD1" <-> "OD2" Residue "A PHE 2912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 16.43, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.87 Conformation dependent library (CDL) restraints added in 5.7 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: 5.46 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: 23.37 Time building geometry restraints manager: 14.13 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: 98.19 - 106.49: 885 106.49 - 114.80: 18611 114.80 - 123.10: 20979 123.10 - 131.41: 1749 131.41 - 139.71: 86 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 2.440 ... (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 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: 1.210 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: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 97.370 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.150 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.620 ------------------------------------------------------------------------------- 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= 0.271 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 3.685 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: 0.3997 time to fit residues: 109.7104 Evaluate side-chains 133 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 3.265 ------------------------------------------------------------------------------- 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: 9.9990 chunk 303 optimal weight: 10.0000 chunk 168 optimal weight: 30.0000 chunk 103 optimal weight: 0.3980 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: 7.9990 chunk 364 optimal weight: 10.0000 overall best weight: 6.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1863 ASN A1894 GLN A2027 ASN A2083 GLN ** A2109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN A2468 ASN A2471 GLN A2781 GLN ** 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 A4108 GLN A4466 HIS ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 31095 Z= 0.302 Angle : 0.631 9.458 42310 Z= 0.328 Chirality : 0.041 0.152 4905 Planarity : 0.005 0.058 5441 Dihedral : 6.912 164.995 4366 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % 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: -0.10 (0.13), residues: 3987 helix: 0.69 (0.11), residues: 2145 sheet: -0.60 (0.24), residues: 462 loop : -0.96 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 135 HIS 0.006 0.001 HIS A2857 PHE 0.027 0.002 PHE A1936 TYR 0.017 0.002 TYR A1618 ARG 0.007 0.001 ARG A2358 *********************** 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 152 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 3.589 Fit side-chains revert: symmetry clash REVERT: A 2461 MET cc_start: 0.8390 (mmp) cc_final: 0.7942 (mmp) REVERT: A 3030 MET cc_start: 0.8651 (mpp) cc_final: 0.8165 (mpp) REVERT: A 3068 MET cc_start: 0.8386 (ptm) cc_final: 0.8180 (ptp) REVERT: A 3791 MET cc_start: 0.9034 (ppp) cc_final: 0.8737 (ppp) REVERT: A 4043 MET cc_start: 0.6983 (tpt) cc_final: 0.6602 (tpt) REVERT: B 188 MET cc_start: 0.7964 (mmm) cc_final: 0.7478 (mmm) outliers start: 2 outliers final: 1 residues processed: 152 average time/residue: 0.3819 time to fit residues: 102.4627 Evaluate side-chains 130 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 202 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 chunk 303 optimal weight: 30.0000 chunk 247 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 364 optimal weight: 6.9990 chunk 394 optimal weight: 9.9990 chunk 324 optimal weight: 5.9990 chunk 361 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 292 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1502 ASN A1612 GLN A1894 GLN ** A2109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3156 GLN A3907 HIS A4012 ASN A4325 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31095 Z= 0.276 Angle : 0.601 9.008 42310 Z= 0.311 Chirality : 0.041 0.157 4905 Planarity : 0.004 0.073 5441 Dihedral : 6.763 163.802 4366 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % 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: 0.53 (0.13), residues: 3987 helix: 1.36 (0.11), residues: 2151 sheet: -0.65 (0.23), residues: 479 loop : -0.84 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A3097 HIS 0.005 0.001 HIS B 233 PHE 0.023 0.002 PHE A1936 TYR 0.015 0.002 TYR A3827 ARG 0.007 0.000 ARG A2492 *********************** 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 156 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.425 Fit side-chains REVERT: A 1579 MET cc_start: 0.8246 (tmm) cc_final: 0.7975 (tmm) REVERT: A 2012 MET cc_start: 0.8251 (mmm) cc_final: 0.7490 (mmm) REVERT: A 2799 MET cc_start: 0.8817 (mpp) cc_final: 0.8352 (mpp) REVERT: A 3030 MET cc_start: 0.8768 (mpp) cc_final: 0.8143 (mpp) REVERT: A 3068 MET cc_start: 0.8489 (ptm) cc_final: 0.8272 (ptp) REVERT: A 3791 MET cc_start: 0.8993 (ppp) cc_final: 0.8721 (ppp) REVERT: A 4043 MET cc_start: 0.7322 (tpt) cc_final: 0.7027 (tpt) REVERT: B 188 MET cc_start: 0.7955 (mmm) cc_final: 0.7482 (mmm) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.3894 time to fit residues: 106.6233 Evaluate side-chains 128 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 360 optimal weight: 7.9990 chunk 274 optimal weight: 10.0000 chunk 189 optimal weight: 0.2980 chunk 40 optimal weight: 5.9990 chunk 174 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 387 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 346 optimal weight: 20.0000 chunk 104 optimal weight: 0.4980 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 A3622 ASN A4079 GLN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31095 Z= 0.188 Angle : 0.543 8.942 42310 Z= 0.276 Chirality : 0.040 0.230 4905 Planarity : 0.004 0.052 5441 Dihedral : 6.505 161.434 4366 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: 1.82 (0.11), residues: 2159 sheet: -0.62 (0.23), residues: 490 loop : -0.79 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 261 HIS 0.008 0.001 HIS C 277 PHE 0.014 0.001 PHE A2343 TYR 0.013 0.001 TYR A1546 ARG 0.005 0.000 ARG C 316 *********************** 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 158 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 3.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8219 (tmm) cc_final: 0.7926 (tmm) REVERT: A 2012 MET cc_start: 0.8088 (mmm) cc_final: 0.7534 (mmm) REVERT: A 3030 MET cc_start: 0.8598 (mpp) cc_final: 0.8254 (mpp) REVERT: A 3068 MET cc_start: 0.8473 (ptm) cc_final: 0.8253 (ptp) REVERT: A 3791 MET cc_start: 0.8975 (ppp) cc_final: 0.8722 (ppp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.3779 time to fit residues: 103.3011 Evaluate side-chains 133 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 322 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 chunk 159 optimal weight: 0.5980 chunk 330 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 197 optimal weight: 6.9990 chunk 347 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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 ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3622 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1997 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= 0.248 Angle : 0.572 9.574 42310 Z= 0.293 Chirality : 0.040 0.194 4905 Planarity : 0.004 0.055 5441 Dihedral : 6.457 161.514 4366 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 1.04 (0.14), residues: 3987 helix: 1.91 (0.11), residues: 2165 sheet: -0.63 (0.23), residues: 493 loop : -0.81 (0.18), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 177 HIS 0.005 0.001 HIS C 277 PHE 0.025 0.002 PHE A2682 TYR 0.012 0.001 TYR A1546 ARG 0.003 0.000 ARG A3695 *********************** 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 151 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8230 (tmm) cc_final: 0.7990 (tmm) REVERT: A 1709 MET cc_start: 0.8976 (ptp) cc_final: 0.8757 (ptp) REVERT: A 2012 MET cc_start: 0.8212 (mmm) cc_final: 0.7398 (mmm) REVERT: A 2799 MET cc_start: 0.8694 (mpp) cc_final: 0.8351 (mpp) REVERT: A 3030 MET cc_start: 0.8732 (mpp) cc_final: 0.8226 (mpp) REVERT: A 3068 MET cc_start: 0.8535 (ptm) cc_final: 0.8318 (ptp) REVERT: A 3126 MET cc_start: 0.8155 (tpt) cc_final: 0.7808 (tpt) REVERT: A 3791 MET cc_start: 0.8968 (ppp) cc_final: 0.8709 (ppp) REVERT: B 188 MET cc_start: 0.7840 (mmm) cc_final: 0.7361 (mmm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.3842 time to fit residues: 102.4789 Evaluate side-chains 129 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 130 optimal weight: 10.0000 chunk 349 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 387 optimal weight: 7.9990 chunk 322 optimal weight: 30.0000 chunk 179 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3622 ASN A3907 HIS A4131 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31095 Z= 0.203 Angle : 0.547 9.527 42310 Z= 0.278 Chirality : 0.040 0.161 4905 Planarity : 0.004 0.057 5441 Dihedral : 6.357 161.152 4366 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 2164 sheet: -0.60 (0.23), residues: 488 loop : -0.75 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 135 HIS 0.003 0.001 HIS C 277 PHE 0.033 0.001 PHE A1945 TYR 0.013 0.001 TYR A1546 ARG 0.006 0.000 ARG A2729 *********************** 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 155 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 3.492 Fit side-chains revert: symmetry clash 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: 0.8227 (mmm) cc_final: 0.7482 (mmm) REVERT: A 3030 MET cc_start: 0.8556 (mpp) cc_final: 0.8063 (mpp) REVERT: A 3068 MET cc_start: 0.8502 (ptm) cc_final: 0.8278 (ptp) REVERT: A 3126 MET cc_start: 0.8176 (tpt) cc_final: 0.7860 (tpt) REVERT: A 3791 MET cc_start: 0.8947 (ppp) cc_final: 0.8687 (ppp) REVERT: B 188 MET cc_start: 0.7816 (mmm) cc_final: 0.7296 (mmm) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.3661 time to fit residues: 100.4943 Evaluate side-chains 130 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 374 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 283 optimal weight: 30.0000 chunk 219 optimal weight: 0.9980 chunk 326 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 A2998 ASN A3156 GLN A3622 ASN ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2159 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= 0.198 Angle : 0.546 9.414 42310 Z= 0.278 Chirality : 0.040 0.181 4905 Planarity : 0.004 0.056 5441 Dihedral : 6.266 160.552 4366 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 1.34 (0.14), residues: 3987 helix: 2.22 (0.11), residues: 2163 sheet: -0.55 (0.23), residues: 480 loop : -0.77 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 135 HIS 0.004 0.001 HIS A1500 PHE 0.016 0.001 PHE A3832 TYR 0.013 0.001 TYR A1546 ARG 0.003 0.000 ARG A2729 *********************** 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 154 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8129 (tmm) cc_final: 0.7900 (tmm) REVERT: A 2012 MET cc_start: 0.8189 (mmm) cc_final: 0.7462 (mmm) REVERT: A 2461 MET cc_start: 0.8295 (mmp) cc_final: 0.7899 (mmp) REVERT: A 2799 MET cc_start: 0.8652 (mpp) cc_final: 0.8282 (mpp) REVERT: A 3030 MET cc_start: 0.8561 (mpp) cc_final: 0.8216 (mpp) REVERT: A 3068 MET cc_start: 0.8501 (ptm) cc_final: 0.8277 (ptp) REVERT: A 3126 MET cc_start: 0.8182 (tpt) cc_final: 0.7883 (tpt) REVERT: A 3524 MET cc_start: 0.7607 (tpp) cc_final: 0.7334 (tpp) REVERT: A 3791 MET cc_start: 0.8948 (ppp) cc_final: 0.8686 (ppp) REVERT: A 4043 MET cc_start: 0.6863 (tpt) cc_final: 0.6511 (tpt) REVERT: B 188 MET cc_start: 0.7857 (mmm) cc_final: 0.7273 (mmm) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.4203 time to fit residues: 115.5061 Evaluate side-chains 129 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 3.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 239 optimal weight: 0.0970 chunk 154 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 116 optimal weight: 0.0570 chunk 75 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 263 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 303 optimal weight: 6.9990 overall best weight: 3.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN A3139 HIS A3622 ASN ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2199 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= 0.171 Angle : 0.532 9.377 42310 Z= 0.269 Chirality : 0.039 0.154 4905 Planarity : 0.003 0.054 5441 Dihedral : 6.154 159.869 4366 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: 1.48 (0.14), residues: 3987 helix: 2.35 (0.11), residues: 2157 sheet: -0.52 (0.23), residues: 492 loop : -0.71 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 177 HIS 0.003 0.001 HIS A3837 PHE 0.037 0.001 PHE A2682 TYR 0.013 0.001 TYR A1546 ARG 0.004 0.000 ARG C 144 *********************** 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 153 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.435 Fit side-chains revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8108 (tmm) cc_final: 0.7885 (tmm) REVERT: A 1685 MET cc_start: 0.8417 (mmm) cc_final: 0.7972 (mmm) REVERT: A 2012 MET cc_start: 0.8233 (mmm) cc_final: 0.7430 (mmm) REVERT: A 2461 MET cc_start: 0.8198 (mmp) cc_final: 0.7849 (mmp) REVERT: A 2799 MET cc_start: 0.8588 (mpp) cc_final: 0.8273 (mpp) REVERT: A 3030 MET cc_start: 0.8698 (mpp) cc_final: 0.8256 (mpp) REVERT: A 3068 MET cc_start: 0.8459 (ptm) cc_final: 0.8238 (ptp) REVERT: A 3126 MET cc_start: 0.8168 (tpt) cc_final: 0.7887 (tpt) REVERT: A 3524 MET cc_start: 0.7690 (tpp) cc_final: 0.7426 (tpp) REVERT: A 3791 MET cc_start: 0.8957 (ppp) cc_final: 0.8716 (ppp) REVERT: A 4043 MET cc_start: 0.6897 (tpt) cc_final: 0.6558 (tpt) REVERT: A 4339 MET cc_start: 0.8686 (ppp) cc_final: 0.8305 (ppp) REVERT: B 188 MET cc_start: 0.7846 (mmm) cc_final: 0.7366 (mmm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3749 time to fit residues: 100.8403 Evaluate side-chains 130 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 351 optimal weight: 0.3980 chunk 370 optimal weight: 7.9990 chunk 337 optimal weight: 0.0670 chunk 360 optimal weight: 7.9990 chunk 216 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 282 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 325 optimal weight: 7.9990 chunk 340 optimal weight: 0.5980 chunk 358 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN A2468 ASN A2689 HIS A3139 HIS A3198 GLN C 389 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31095 Z= 0.129 Angle : 0.511 10.402 42310 Z= 0.256 Chirality : 0.039 0.175 4905 Planarity : 0.003 0.053 5441 Dihedral : 5.901 156.643 4366 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: 1.71 (0.14), residues: 3987 helix: 2.55 (0.11), residues: 2154 sheet: -0.33 (0.23), residues: 472 loop : -0.68 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 177 HIS 0.004 0.001 HIS A4389 PHE 0.034 0.001 PHE A2682 TYR 0.037 0.001 TYR A3026 ARG 0.003 0.000 ARG A1710 *********************** 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 157 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8076 (tmm) cc_final: 0.7856 (tmm) REVERT: A 1685 MET cc_start: 0.8475 (mmm) cc_final: 0.8117 (mmm) REVERT: A 1941 MET cc_start: 0.8482 (tpt) cc_final: 0.8241 (mmt) REVERT: A 2012 MET cc_start: 0.8153 (mmm) cc_final: 0.7222 (mmm) REVERT: A 2461 MET cc_start: 0.8106 (mmp) cc_final: 0.7720 (mmp) REVERT: A 3068 MET cc_start: 0.8351 (ptm) cc_final: 0.8148 (ptp) REVERT: A 3126 MET cc_start: 0.8044 (tpt) cc_final: 0.7745 (tpt) REVERT: A 3524 MET cc_start: 0.7775 (tpp) cc_final: 0.7522 (tpp) REVERT: A 3791 MET cc_start: 0.8959 (ppp) cc_final: 0.8710 (ppp) REVERT: B 188 MET cc_start: 0.7831 (mmm) cc_final: 0.7330 (mmm) REVERT: C 123 MET cc_start: 0.8890 (ppp) cc_final: 0.8454 (ppp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3789 time to fit residues: 104.4016 Evaluate side-chains 131 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 236 optimal weight: 7.9990 chunk 380 optimal weight: 0.0010 chunk 232 optimal weight: 0.0670 chunk 180 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 399 optimal weight: 20.0000 chunk 367 optimal weight: 9.9990 chunk 318 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 overall best weight: 3.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1646 ASN ** A1855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31095 Z= 0.172 Angle : 0.525 10.053 42310 Z= 0.264 Chirality : 0.039 0.166 4905 Planarity : 0.003 0.051 5441 Dihedral : 5.860 156.082 4366 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 1.75 (0.14), residues: 3987 helix: 2.59 (0.11), residues: 2155 sheet: -0.34 (0.23), residues: 472 loop : -0.67 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 177 HIS 0.003 0.001 HIS C 193 PHE 0.017 0.001 PHE A4268 TYR 0.034 0.001 TYR A3026 ARG 0.007 0.000 ARG A2684 ********************** 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 152 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 3.719 Fit side-chains revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8138 (tmm) cc_final: 0.7936 (tmm) REVERT: A 1941 MET cc_start: 0.8538 (tpt) cc_final: 0.8247 (mmt) REVERT: A 2012 MET cc_start: 0.8174 (mmm) cc_final: 0.7375 (mmm) REVERT: A 2461 MET cc_start: 0.8177 (mmp) cc_final: 0.7806 (mmp) REVERT: A 3126 MET cc_start: 0.8115 (tpt) cc_final: 0.7824 (tpt) REVERT: A 3524 MET cc_start: 0.7807 (tpp) cc_final: 0.7579 (tpp) REVERT: A 3791 MET cc_start: 0.8948 (ppp) cc_final: 0.8703 (ppp) REVERT: A 4095 MET cc_start: 0.6586 (tpp) cc_final: 0.6127 (tpp) REVERT: A 4339 MET cc_start: 0.8665 (ppp) cc_final: 0.8359 (ppp) REVERT: B 188 MET cc_start: 0.7877 (mmm) cc_final: 0.7333 (mmm) REVERT: C 123 MET cc_start: 0.8891 (ppp) cc_final: 0.8457 (ppp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.3811 time to fit residues: 102.9205 Evaluate side-chains 132 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 252 optimal weight: 0.4980 chunk 338 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 293 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 318 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 327 optimal weight: 40.0000 chunk 40 optimal weight: 0.0870 chunk 58 optimal weight: 10.0000 overall best weight: 2.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1646 ASN ** A1855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** B 154 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 = 0.3347 r_free = 0.3347 target = 0.039288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.033434 restraints weight = 367057.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.034187 restraints weight = 210059.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.034426 restraints weight = 125642.637| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31095 Z= 0.147 Angle : 0.518 9.992 42310 Z= 0.260 Chirality : 0.039 0.160 4905 Planarity : 0.003 0.048 5441 Dihedral : 5.814 155.471 4366 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: 1.78 (0.14), residues: 3987 helix: 2.61 (0.11), residues: 2160 sheet: -0.31 (0.23), residues: 472 loop : -0.66 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A2500 HIS 0.002 0.001 HIS C 193 PHE 0.034 0.001 PHE A2682 TYR 0.031 0.001 TYR A3026 ARG 0.005 0.000 ARG A2684 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4628.08 seconds wall clock time: 85 minutes 16.40 seconds (5116.40 seconds total)