Starting phenix.real_space_refine on Sun Apr 14 05:10:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqw_17826/04_2024/8pqw_17826_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqw_17826/04_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_17826/04_2024/8pqw_17826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqw_17826/04_2024/8pqw_17826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqw_17826/04_2024/8pqw_17826_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqw_17826/04_2024/8pqw_17826_updated.pdb" } 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 15.74, per 1000 atoms: 0.52 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: 11.60 Conformation dependent library (CDL) restraints added in 5.4 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... running ksdssp... Secondary structure from input PDB file: 128 helices and 31 sheets defined 51.1% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.02 Creating SS restraints... Processing helix chain 'A' and resid 1445 through 1471 Processing helix chain 'A' and resid 1491 through 1509 removed outlier: 3.798A pdb=" N LEU A1509 " --> pdb=" O SER A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1553 removed outlier: 3.606A pdb=" N GLU A1517 " --> pdb=" O LYS A1514 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU A1518 " --> pdb=" O VAL A1515 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP A1519 " --> pdb=" O PHE A1516 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A1520 " --> pdb=" O GLU A1517 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A1538 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A1541 " --> pdb=" O ILE A1538 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A1545 " --> pdb=" O ARG A1542 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A1547 " --> pdb=" O TRP A1544 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A1552 " --> pdb=" O GLY A1549 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A1553 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1584 Processing helix chain 'A' and resid 1588 through 1592 Processing helix chain 'A' and resid 1597 through 1613 Processing helix chain 'A' and resid 1616 through 1625 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 1628 through 1631 Processing helix chain 'A' and resid 1634 through 1642 Processing helix chain 'A' and resid 1650 through 1652 No H-bonds generated for 'chain 'A' and resid 1650 through 1652' Processing helix chain 'A' and resid 1654 through 1657 No H-bonds generated for 'chain 'A' and resid 1654 through 1657' Processing helix chain 'A' and resid 1698 through 1728 removed outlier: 3.944A pdb=" N ARG A1710 " --> pdb=" O GLU A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1744 Processing helix chain 'A' and resid 1747 through 1767 Processing helix chain 'A' and resid 1776 through 1796 Processing helix chain 'A' and resid 1802 through 1827 Processing helix chain 'A' and resid 1836 through 1839 No H-bonds generated for 'chain 'A' and resid 1836 through 1839' Processing helix chain 'A' and resid 1853 through 1855 No H-bonds generated for 'chain 'A' and resid 1853 through 1855' Processing helix chain 'A' and resid 1883 through 1897 Processing helix chain 'A' and resid 1913 through 1922 Processing helix chain 'A' and resid 1938 through 1951 Processing helix chain 'A' and resid 1965 through 1985 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 2030 through 2035 removed outlier: 3.811A pdb=" N LEU A2035 " --> pdb=" O ASN A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2046 through 2057 Processing helix chain 'A' and resid 2062 through 2079 Proline residue: A2071 - end of helix removed outlier: 3.769A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2090 through 2113 removed outlier: 3.782A pdb=" N SER A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) Processing helix chain 'A' and resid 2133 through 2145 Processing helix chain 'A' and resid 2154 through 2164 Processing helix chain 'A' and resid 2176 through 2188 Processing helix chain 'A' and resid 2201 through 2216 Processing helix chain 'A' and resid 2230 through 2245 removed outlier: 3.988A pdb=" N TRP A2234 " --> pdb=" O LYS A2230 " (cutoff:3.500A) Processing helix chain 'A' and resid 2262 through 2265 No H-bonds generated for 'chain 'A' and resid 2262 through 2265' Processing helix chain 'A' and resid 2279 through 2289 Processing helix chain 'A' and resid 2312 through 2314 No H-bonds generated for 'chain 'A' and resid 2312 through 2314' Processing helix chain 'A' and resid 2353 through 2356 No H-bonds generated for 'chain 'A' and resid 2353 through 2356' Processing helix chain 'A' and resid 2371 through 2383 Processing helix chain 'A' and resid 2411 through 2427 Proline residue: A2425 - end of helix Processing helix chain 'A' and resid 2433 through 2442 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) Processing helix chain 'A' and resid 2451 through 2475 Processing helix chain 'A' and resid 2483 through 2503 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 2508 through 2521 Processing helix chain 'A' and resid 2534 through 2536 No H-bonds generated for 'chain 'A' and resid 2534 through 2536' Processing helix chain 'A' and resid 2548 through 2551 No H-bonds generated for 'chain 'A' and resid 2548 through 2551' Processing helix chain 'A' and resid 2572 through 2587 removed outlier: 4.459A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2603 through 2611 removed outlier: 3.759A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2638 Processing helix chain 'A' and resid 2678 through 2688 Processing helix chain 'A' and resid 2725 through 2728 No H-bonds generated for 'chain 'A' and resid 2725 through 2728' Processing helix chain 'A' and resid 2741 through 2755 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 2762 through 2780 removed outlier: 4.784A pdb=" N GLU A2767 " --> pdb=" O THR A2764 " (cutoff:3.500A) Proline residue: A2768 - end of helix removed outlier: 4.634A pdb=" N PHE A2776 " --> pdb=" O MET A2773 " (cutoff:3.500A) Processing helix chain 'A' and resid 2796 through 2810 Processing helix chain 'A' and resid 2818 through 2833 Processing helix chain 'A' and resid 2840 through 2857 Processing helix chain 'A' and resid 2863 through 2866 No H-bonds generated for 'chain 'A' and resid 2863 through 2866' Processing helix chain 'A' and resid 2886 through 2902 removed outlier: 4.070A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2913 through 2927 Processing helix chain 'A' and resid 2943 through 2953 Processing helix chain 'A' and resid 2969 through 2984 Processing helix chain 'A' and resid 3002 through 3014 Processing helix chain 'A' and resid 3024 through 3040 Processing helix chain 'A' and resid 3048 through 3061 Processing helix chain 'A' and resid 3074 through 3081 removed outlier: 3.529A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3084 through 3087 No H-bonds generated for 'chain 'A' and resid 3084 through 3087' Processing helix chain 'A' and resid 3099 through 3109 Processing helix chain 'A' and resid 3139 through 3164 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) Processing helix chain 'A' and resid 3173 through 3239 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 3501 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 3503 through 3515 removed outlier: 3.506A pdb=" N LEU A3509 " --> pdb=" O GLY A3505 " (cutoff:3.500A) Processing helix chain 'A' and resid 3522 through 3538 Processing helix chain 'A' and resid 3549 through 3553 removed outlier: 3.820A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3549 through 3553' Processing helix chain 'A' and resid 3556 through 3564 Processing helix chain 'A' and resid 3571 through 3581 Processing helix chain 'A' and resid 3595 through 3603 Processing helix chain 'A' and resid 3620 through 3629 Processing helix chain 'A' and resid 3643 through 3649 Proline residue: A3647 - end of helix Processing helix chain 'A' and resid 3690 through 3695 removed outlier: 3.850A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) Processing helix chain 'A' and resid 3705 through 3720 Processing helix chain 'A' and resid 3722 through 3754 Processing helix chain 'A' and resid 3765 through 3822 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 removed outlier: 4.432A pdb=" N LYS A3819 " --> pdb=" O MET A3815 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLN A3820 " --> pdb=" O GLU A3816 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE A3821 " --> pdb=" O SER A3817 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N HIS A3822 " --> pdb=" O LEU A3818 " (cutoff:3.500A) Processing helix chain 'A' and resid 3829 through 3840 Processing helix chain 'A' and resid 3852 through 3874 removed outlier: 3.901A pdb=" N SER A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3894 removed outlier: 3.550A pdb=" N HIS A3880 " --> pdb=" O HIS A3877 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE A3881 " --> pdb=" O GLN A3878 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A3882 " --> pdb=" O ASP A3879 " (cutoff:3.500A) Processing helix chain 'A' and resid 3902 through 3910 Processing helix chain 'A' and resid 3929 through 3940 removed outlier: 3.895A pdb=" N CYS A3940 " --> pdb=" O VAL A3936 " (cutoff:3.500A) Processing helix chain 'A' and resid 3947 through 3953 removed outlier: 3.633A pdb=" N GLN A3952 " --> pdb=" O ILE A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3982 through 3996 Processing helix chain 'A' and resid 3998 through 4012 removed outlier: 4.374A pdb=" N LEU A4002 " --> pdb=" O ASP A3999 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A4007 " --> pdb=" O MET A4004 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A4011 " --> pdb=" O PHE A4008 " (cutoff:3.500A) Processing helix chain 'A' and resid 4027 through 4033 Processing helix chain 'A' and resid 4052 through 4061 Processing helix chain 'A' and resid 4074 through 4089 Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4103 through 4114 removed outlier: 4.115A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) Processing helix chain 'A' and resid 4136 through 4140 Processing helix chain 'A' and resid 4153 through 4163 Processing helix chain 'A' and resid 4166 through 4169 No H-bonds generated for 'chain 'A' and resid 4166 through 4169' Processing helix chain 'A' and resid 4174 through 4193 removed outlier: 4.175A pdb=" N ALA A4177 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A4190 " --> pdb=" O HIS A4187 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A4192 " --> pdb=" O ILE A4189 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A4193 " --> pdb=" O ILE A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4209 through 4226 Processing helix chain 'A' and resid 4240 through 4249 Processing helix chain 'A' and resid 4259 through 4272 Processing helix chain 'A' and resid 4275 through 4278 No H-bonds generated for 'chain 'A' and resid 4275 through 4278' Processing helix chain 'A' and resid 4302 through 4310 Processing helix chain 'A' and resid 4318 through 4321 Processing helix chain 'A' and resid 4329 through 4347 Processing helix chain 'A' and resid 4380 through 4394 Proline residue: A4392 - end of helix Processing helix chain 'A' and resid 4408 through 4438 Processing helix chain 'A' and resid 4446 through 4457 Processing helix chain 'A' and resid 4475 through 4497 removed outlier: 3.671A pdb=" N SER A4480 " --> pdb=" O ILE A4476 " (cutoff:3.500A) Processing helix chain 'A' and resid 4517 through 4532 Processing helix chain 'A' and resid 4632 through 4637 Processing helix chain 'B' and resid 287 through 296 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 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 287 through 296 removed outlier: 4.385A pdb=" N SER C 291 " --> pdb=" O SER C 288 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE C 293 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 21 Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 50 through 74 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 5 through 21 Processing helix chain 'E' and resid 25 through 34 Processing helix chain 'E' and resid 41 through 47 removed outlier: 3.578A pdb=" N LYS E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 47' Processing helix chain 'E' and resid 50 through 56 Processing helix chain 'E' and resid 58 through 74 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 397 through 436 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) Processing helix chain 'F' and resid 439 through 467 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 470 through 540 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 397 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 437 through 542 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) Processing helix chain 'H' and resid 4 through 34 Processing helix chain 'I' and resid 4 through 33 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= A, 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= B, first strand: chain 'A' and resid 1683 through 1685 removed outlier: 6.413A pdb=" N ILE A1665 " --> pdb=" O LEU A1674 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE A1676 " --> pdb=" O SER A1663 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER A1663 " --> pdb=" O ILE A1676 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id= D, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id= E, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 6.454A pdb=" N TRP A1954 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE A1930 " --> pdb=" O TRP A1954 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N CYS A1956 " --> pdb=" O PHE A1930 " (cutoff:3.500A) Processing sheet with id= F, 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= G, first strand: chain 'A' and resid 2360 through 2364 removed outlier: 8.758A pdb=" N LEU A2220 " --> pdb=" O VAL A2339 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A2341 " --> pdb=" O LEU A2220 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N MET A2222 " --> pdb=" O ILE A2341 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A2343 " --> pdb=" O MET A2222 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLY A2224 " --> pdb=" O PHE A2343 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id= I, first strand: chain 'A' and resid 2732 through 2735 removed outlier: 3.660A pdb=" N LEU A2591 " --> pdb=" O PHE A2708 " (cutoff:3.500A) 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) Processing sheet with id= J, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 4.378A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 3090 through 3093 removed outlier: 6.541A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) 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) Processing sheet with id= L, first strand: chain 'A' and resid 3697 through 3700 removed outlier: 7.039A pdb=" N ILE A3677 " --> pdb=" O PRO A3587 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE A3589 " --> pdb=" O ILE A3677 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU A3679 " --> pdb=" O ILE A3589 " (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: 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) Processing sheet with id= M, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id= N, first strand: chain 'A' and resid 4143 through 4147 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) Processing sheet with id= O, first strand: chain 'A' and resid 4540 through 4544 Processing sheet with id= P, first strand: chain 'A' and resid 4568 through 4571 Processing sheet with id= Q, first strand: chain 'A' and resid 4604 through 4610 removed outlier: 3.922A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 102 through 105 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= S, first strand: chain 'B' and resid 111 through 116 removed outlier: 6.952A pdb=" N ALA B 126 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL B 114 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 124 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASP B 136 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE B 142 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 153 through 158 removed outlier: 6.936A pdb=" N CYS B 168 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE B 156 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA B 166 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B 158 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 164 " --> pdb=" O PHE B 158 " (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: 5.407A pdb=" N ASP B 178 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N CYS B 184 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing sheet with id= U, 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= V, first strand: chain 'B' and resid 237 through 242 removed outlier: 7.052A pdb=" N CYS B 252 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL B 240 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA B 250 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 248 " --> pdb=" O PRO B 242 " (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= W, first strand: chain 'B' and resid 279 through 284 removed outlier: 6.830A pdb=" N GLY B 314 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE B 282 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 312 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TRP B 284 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE B 310 " --> pdb=" O TRP B 284 " (cutoff:3.500A) 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: 3.628A pdb=" N MET B 332 " --> pdb=" O MET B 322 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASP B 324 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYS B 330 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 341 through 346 removed outlier: 6.713A pdb=" N CYS B 356 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL B 344 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 354 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE B 346 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE B 352 " --> pdb=" O PHE B 346 " (cutoff:3.500A) 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= Y, first strand: chain 'C' and resid 102 through 105 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= Z, first strand: chain 'C' and resid 111 through 116 removed outlier: 6.932A pdb=" N ALA C 126 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL C 114 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 124 " --> pdb=" O VAL C 114 " (cutoff:3.500A) 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= AA, 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= AB, first strand: chain 'C' and resid 195 through 200 removed outlier: 6.842A pdb=" N ALA C 210 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 198 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 208 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE C 200 " --> pdb=" O HIS C 206 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N HIS C 206 " --> pdb=" O ILE C 200 " (cutoff:3.500A) 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= AC, first strand: chain 'C' and resid 237 through 242 removed outlier: 6.974A pdb=" N CYS C 252 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL C 240 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA C 250 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU C 248 " --> pdb=" O PRO C 242 " (cutoff:3.500A) 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= AD, first strand: chain 'C' and resid 279 through 284 removed outlier: 6.820A pdb=" N GLY C 314 " --> pdb=" O GLU C 280 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE C 282 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 312 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TRP C 284 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE C 310 " --> pdb=" O TRP C 284 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET C 332 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASP C 324 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS C 330 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 341 through 346 removed outlier: 6.736A pdb=" N CYS C 356 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL C 344 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 354 " --> pdb=" O VAL C 344 " (cutoff:3.500A) 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) 1665 hydrogen bonds defined for protein. 4686 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: 20.09 Time building geometry restraints manager: 12.43 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: 117 2.45 - 3.07: 18280 3.07 - 3.68: 49537 3.68 - 4.29: 69210 4.29 - 4.90: 111580 Nonbonded interactions: 248724 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 248719 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: 1.050 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: 0.030 Extract box with map and model: 6.590 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 88.080 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.570 ------------------------------------------------------------------------------- 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= 0.275 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 : 3.697 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: 0.3973 time to fit residues: 107.8128 Evaluate side-chains 133 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 3.490 ------------------------------------------------------------------------------- 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: 8.9990 chunk 168 optimal weight: 40.0000 chunk 103 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 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: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 A2827 HIS A2930 GLN A2964 HIS ** A2998 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 A4079 GLN 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 31095 Z= 0.343 Angle : 0.665 9.716 42310 Z= 0.346 Chirality : 0.041 0.150 4905 Planarity : 0.005 0.057 5441 Dihedral : 7.025 164.648 4366 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.17 % Allowed : 6.16 % Favored : 93.67 % 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: -0.27 (0.13), residues: 3987 helix: 0.52 (0.11), residues: 2115 sheet: -0.51 (0.24), residues: 456 loop : -1.00 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 323 HIS 0.005 0.001 HIS A4006 PHE 0.032 0.002 PHE A1936 TYR 0.017 0.002 TYR B 394 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 154 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 4.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2012 MET cc_start: 0.8118 (mmm) cc_final: 0.7472 (mmm) REVERT: A 3008 MET cc_start: 0.9399 (mmm) cc_final: 0.9193 (tpp) REVERT: A 3030 MET cc_start: 0.8669 (mpp) cc_final: 0.8165 (mpp) REVERT: A 3791 MET cc_start: 0.9020 (ppp) cc_final: 0.8716 (ppp) outliers start: 5 outliers final: 3 residues processed: 154 average time/residue: 0.3991 time to fit residues: 110.2755 Evaluate side-chains 131 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 3.703 ------------------------------------------------------------------------------- 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: 5.9990 chunk 113 optimal weight: 0.0070 chunk 303 optimal weight: 20.0000 chunk 247 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 364 optimal weight: 6.9990 chunk 394 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 chunk 361 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 292 optimal weight: 7.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1502 ASN ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN A2468 ASN A2930 GLN ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3156 GLN A3907 HIS A4325 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31095 Z= 0.210 Angle : 0.554 8.557 42310 Z= 0.285 Chirality : 0.040 0.176 4905 Planarity : 0.004 0.079 5441 Dihedral : 6.740 163.584 4366 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: 0.41 (0.13), residues: 3987 helix: 1.22 (0.11), residues: 2126 sheet: -0.50 (0.24), residues: 455 loop : -0.85 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 135 HIS 0.003 0.001 HIS B 233 PHE 0.022 0.001 PHE C 346 TYR 0.014 0.001 TYR A1546 ARG 0.009 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 : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8210 (tmm) cc_final: 0.7914 (tmm) REVERT: A 2012 MET cc_start: 0.8083 (mmm) cc_final: 0.7171 (mmm) REVERT: A 2799 MET cc_start: 0.8708 (mpp) cc_final: 0.8298 (mpp) REVERT: A 3008 MET cc_start: 0.9356 (mmm) cc_final: 0.9127 (tpp) REVERT: A 3030 MET cc_start: 0.8635 (mpp) cc_final: 0.8101 (mpp) REVERT: A 3068 MET cc_start: 0.8724 (ptp) cc_final: 0.8427 (ptp) REVERT: A 3126 MET cc_start: 0.8008 (tpt) cc_final: 0.7667 (tpt) REVERT: A 3524 MET cc_start: 0.7876 (tpp) cc_final: 0.7615 (tpp) REVERT: A 3791 MET cc_start: 0.8980 (ppp) cc_final: 0.8705 (ppp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.4012 time to fit residues: 109.6326 Evaluate side-chains 131 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.583 ------------------------------------------------------------------------------- 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: 50.0000 chunk 274 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 174 optimal weight: 30.0000 chunk 244 optimal weight: 3.9990 chunk 366 optimal weight: 7.9990 chunk 387 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 346 optimal weight: 30.0000 chunk 104 optimal weight: 0.0050 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1614 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= 0.188 Angle : 0.530 8.972 42310 Z= 0.270 Chirality : 0.039 0.224 4905 Planarity : 0.004 0.054 5441 Dihedral : 6.523 161.827 4366 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.14), residues: 3987 helix: 1.65 (0.11), residues: 2118 sheet: -0.53 (0.23), residues: 495 loop : -0.72 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 261 HIS 0.014 0.001 HIS C 277 PHE 0.015 0.001 PHE A4147 TYR 0.015 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 156 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8198 (tmm) cc_final: 0.7892 (tmm) REVERT: A 1709 MET cc_start: 0.8912 (ptp) cc_final: 0.8683 (ptp) REVERT: A 2012 MET cc_start: 0.8098 (mmm) cc_final: 0.7525 (mmm) REVERT: A 3008 MET cc_start: 0.9331 (mmm) cc_final: 0.9113 (tpp) REVERT: A 3030 MET cc_start: 0.8641 (mpp) cc_final: 0.8261 (mpp) REVERT: A 3068 MET cc_start: 0.8804 (ptp) cc_final: 0.8504 (ptp) REVERT: A 3126 MET cc_start: 0.8084 (tpt) cc_final: 0.7793 (tpt) REVERT: A 3500 MET cc_start: 0.7511 (tmm) cc_final: 0.6899 (tmm) REVERT: A 3524 MET cc_start: 0.7849 (tpp) cc_final: 0.7576 (tpp) REVERT: A 3791 MET cc_start: 0.8973 (ppp) cc_final: 0.8728 (ppp) REVERT: B 188 MET cc_start: 0.7626 (mmm) cc_final: 0.7385 (mmt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.4142 time to fit residues: 112.2433 Evaluate side-chains 130 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.750 ------------------------------------------------------------------------------- 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: 40.0000 chunk 220 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 288 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 330 optimal weight: 20.0000 chunk 267 optimal weight: 0.0470 chunk 0 optimal weight: 40.0000 chunk 197 optimal weight: 0.0670 chunk 347 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 overall best weight: 4.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN A2377 ASN A2468 ASN A2471 GLN ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3156 GLN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31095 Z= 0.217 Angle : 0.547 9.614 42310 Z= 0.279 Chirality : 0.040 0.184 4905 Planarity : 0.004 0.053 5441 Dihedral : 6.421 161.224 4366 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: 0.97 (0.14), residues: 3987 helix: 1.80 (0.11), residues: 2124 sheet: -0.48 (0.23), residues: 481 loop : -0.73 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A4592 HIS 0.004 0.001 HIS B 233 PHE 0.034 0.001 PHE A3832 TYR 0.015 0.001 TYR A1546 ARG 0.008 0.000 ARG A2729 *********************** 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 154 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 4.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8202 (tmm) cc_final: 0.7954 (tmm) REVERT: A 2012 MET cc_start: 0.8183 (mmm) cc_final: 0.7304 (mmm) REVERT: A 2510 MET cc_start: 0.8559 (tpp) cc_final: 0.8347 (tpp) REVERT: A 3008 MET cc_start: 0.9341 (mmm) cc_final: 0.9127 (tpp) REVERT: A 3030 MET cc_start: 0.8626 (mpp) cc_final: 0.8126 (mpp) REVERT: A 3068 MET cc_start: 0.8830 (ptp) cc_final: 0.8568 (ptp) REVERT: A 3126 MET cc_start: 0.8142 (tpt) cc_final: 0.7873 (tpt) REVERT: A 3524 MET cc_start: 0.7942 (tpp) cc_final: 0.7668 (tpp) REVERT: A 3791 MET cc_start: 0.8955 (ppp) cc_final: 0.8702 (ppp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3987 time to fit residues: 109.1751 Evaluate side-chains 130 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.934 ------------------------------------------------------------------------------- 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: 5.9990 chunk 349 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 227 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 387 optimal weight: 7.9990 chunk 322 optimal weight: 50.0000 chunk 179 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2377 ASN A2468 ASN ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3622 ASN A4006 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1921 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= 0.195 Angle : 0.530 9.514 42310 Z= 0.270 Chirality : 0.039 0.152 4905 Planarity : 0.004 0.049 5441 Dihedral : 6.312 160.717 4366 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 1.12 (0.14), residues: 3987 helix: 1.94 (0.11), residues: 2125 sheet: -0.44 (0.23), residues: 493 loop : -0.70 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 135 HIS 0.004 0.001 HIS C 277 PHE 0.027 0.001 PHE A2682 TYR 0.017 0.001 TYR A1546 ARG 0.007 0.000 ARG C 144 *********************** 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 : 3.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8108 (tmm) cc_final: 0.7879 (tmm) REVERT: A 2012 MET cc_start: 0.8230 (mmm) cc_final: 0.7349 (mmm) REVERT: A 2510 MET cc_start: 0.8570 (tpp) cc_final: 0.8315 (tpp) REVERT: A 3008 MET cc_start: 0.9358 (mmm) cc_final: 0.9109 (tpp) REVERT: A 3030 MET cc_start: 0.8651 (mpp) cc_final: 0.8084 (mpp) REVERT: A 3068 MET cc_start: 0.8869 (ptp) cc_final: 0.8629 (ptp) REVERT: A 3126 MET cc_start: 0.8169 (tpt) cc_final: 0.7926 (tpt) REVERT: A 3500 MET cc_start: 0.7590 (tmm) cc_final: 0.6975 (tmm) REVERT: A 3524 MET cc_start: 0.7966 (tpp) cc_final: 0.7692 (tpp) REVERT: A 3791 MET cc_start: 0.8950 (ppp) cc_final: 0.8697 (ppp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.4087 time to fit residues: 111.9104 Evaluate side-chains 129 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 3.892 ------------------------------------------------------------------------------- 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: 0.3980 chunk 221 optimal weight: 8.9990 chunk 283 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 386 optimal weight: 5.9990 chunk 241 optimal weight: 0.0040 chunk 235 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 overall best weight: 3.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2377 ASN A2468 ASN A2471 GLN ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3139 HIS A3622 ASN ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3907 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31095 Z= 0.195 Angle : 0.537 9.347 42310 Z= 0.272 Chirality : 0.039 0.180 4905 Planarity : 0.004 0.050 5441 Dihedral : 6.240 160.567 4366 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 1.18 (0.14), residues: 3987 helix: 2.01 (0.11), residues: 2134 sheet: -0.41 (0.23), residues: 494 loop : -0.72 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 135 HIS 0.004 0.001 HIS A3837 PHE 0.029 0.001 PHE A2682 TYR 0.032 0.001 TYR A3026 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 156 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.541 Fit side-chains revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8122 (tmm) cc_final: 0.7909 (tmm) REVERT: A 2012 MET cc_start: 0.8168 (mmm) cc_final: 0.7276 (mmm) REVERT: A 2461 MET cc_start: 0.8280 (mmp) cc_final: 0.7905 (mmp) REVERT: A 2510 MET cc_start: 0.8611 (tpp) cc_final: 0.8276 (tpp) REVERT: A 2799 MET cc_start: 0.8698 (mpp) cc_final: 0.8289 (mpp) REVERT: A 3008 MET cc_start: 0.9348 (mmm) cc_final: 0.9119 (tpp) REVERT: A 3068 MET cc_start: 0.8890 (ptp) cc_final: 0.8664 (ptp) REVERT: A 3126 MET cc_start: 0.8182 (tpt) cc_final: 0.7948 (tpt) REVERT: A 3500 MET cc_start: 0.7551 (tmm) cc_final: 0.6911 (tmm) REVERT: A 3524 MET cc_start: 0.7977 (tpp) cc_final: 0.7693 (tpp) REVERT: A 3791 MET cc_start: 0.8963 (ppp) cc_final: 0.8720 (ppp) REVERT: A 4339 MET cc_start: 0.8590 (ppp) cc_final: 0.8327 (ppp) REVERT: B 188 MET cc_start: 0.7653 (mmm) cc_final: 0.7405 (mmt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.3922 time to fit residues: 108.5680 Evaluate side-chains 131 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.810 ------------------------------------------------------------------------------- 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: 7.9990 chunk 154 optimal weight: 6.9990 chunk 230 optimal weight: 0.4980 chunk 116 optimal weight: 0.2980 chunk 75 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 303 optimal weight: 8.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2047 GLN A2377 ASN A2468 ASN A2857 HIS ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 31095 Z= 0.155 Angle : 0.518 9.272 42310 Z= 0.260 Chirality : 0.039 0.154 4905 Planarity : 0.003 0.049 5441 Dihedral : 6.115 159.703 4366 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: 2.15 (0.11), residues: 2126 sheet: -0.28 (0.23), residues: 483 loop : -0.67 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 135 HIS 0.003 0.001 HIS C 193 PHE 0.011 0.001 PHE A3004 TYR 0.033 0.001 TYR A3026 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 : 3.404 Fit side-chains revert: symmetry clash REVERT: A 1579 MET cc_start: 0.8066 (tmm) cc_final: 0.7844 (tmm) REVERT: A 1685 MET cc_start: 0.8467 (mmm) cc_final: 0.8028 (mmm) REVERT: A 2012 MET cc_start: 0.8135 (mmm) cc_final: 0.7260 (mmm) REVERT: A 2461 MET cc_start: 0.8184 (mmp) cc_final: 0.7843 (mmp) REVERT: A 3008 MET cc_start: 0.9326 (mmm) cc_final: 0.9117 (tpp) REVERT: A 3030 MET cc_start: 0.8271 (mpp) cc_final: 0.7819 (mpp) REVERT: A 3068 MET cc_start: 0.8900 (ptp) cc_final: 0.8678 (ptp) REVERT: A 3500 MET cc_start: 0.7615 (tmm) cc_final: 0.6958 (tmm) REVERT: A 3524 MET cc_start: 0.7947 (tpp) cc_final: 0.7679 (tpp) REVERT: A 3791 MET cc_start: 0.8949 (ppp) cc_final: 0.8709 (ppp) REVERT: A 4339 MET cc_start: 0.8588 (ppp) cc_final: 0.8380 (ppp) REVERT: B 188 MET cc_start: 0.7584 (mmm) cc_final: 0.7332 (mmt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.4035 time to fit residues: 109.2228 Evaluate side-chains 135 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 3.948 ------------------------------------------------------------------------------- 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: 7.9990 chunk 370 optimal weight: 7.9990 chunk 337 optimal weight: 4.9990 chunk 360 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 282 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 325 optimal weight: 4.9990 chunk 340 optimal weight: 7.9990 chunk 358 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31095 Z= 0.181 Angle : 0.527 10.197 42310 Z= 0.266 Chirality : 0.039 0.163 4905 Planarity : 0.003 0.049 5441 Dihedral : 6.067 159.426 4366 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 1.39 (0.14), residues: 3987 helix: 2.19 (0.11), residues: 2126 sheet: -0.16 (0.23), residues: 471 loop : -0.69 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 177 HIS 0.003 0.001 HIS C 277 PHE 0.030 0.001 PHE A4268 TYR 0.028 0.001 TYR A3026 ARG 0.004 0.000 ARG C 144 *********************** 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 153 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2012 MET cc_start: 0.8203 (mmm) cc_final: 0.7477 (mmm) REVERT: A 2461 MET cc_start: 0.8156 (mmp) cc_final: 0.7813 (mmp) REVERT: A 2510 MET cc_start: 0.8534 (tpp) cc_final: 0.8315 (tpp) REVERT: A 3008 MET cc_start: 0.9314 (mmm) cc_final: 0.9105 (tpp) REVERT: A 3030 MET cc_start: 0.8321 (mpp) cc_final: 0.7902 (mpp) REVERT: A 3068 MET cc_start: 0.8864 (ptp) cc_final: 0.8647 (ptp) REVERT: A 3500 MET cc_start: 0.7621 (tmm) cc_final: 0.7213 (tmm) REVERT: A 3524 MET cc_start: 0.7963 (tpp) cc_final: 0.7698 (tpp) REVERT: A 3791 MET cc_start: 0.8953 (ppp) cc_final: 0.8712 (ppp) REVERT: A 4128 MET cc_start: 0.7729 (pmm) cc_final: 0.6489 (pmm) REVERT: B 188 MET cc_start: 0.7591 (mmm) cc_final: 0.7322 (mmt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.4102 time to fit residues: 110.8082 Evaluate side-chains 130 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.437 ------------------------------------------------------------------------------- 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: 10.0000 chunk 380 optimal weight: 0.0870 chunk 232 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 399 optimal weight: 8.9990 chunk 367 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 overall best weight: 3.2164 ------------------------------------------------------------------------------- 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** A1881 GLN A2377 ASN ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7647 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31095 Z= 0.176 Angle : 0.530 9.909 42310 Z= 0.266 Chirality : 0.039 0.159 4905 Planarity : 0.003 0.049 5441 Dihedral : 6.028 159.127 4366 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: 1.44 (0.14), residues: 3987 helix: 2.23 (0.11), residues: 2121 sheet: -0.23 (0.23), residues: 484 loop : -0.62 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 177 HIS 0.003 0.001 HIS C 277 PHE 0.033 0.001 PHE A2682 TYR 0.029 0.001 TYR A3836 ARG 0.004 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 151 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8386 (mmm) cc_final: 0.7889 (mmm) REVERT: A 2012 MET cc_start: 0.8204 (mmm) cc_final: 0.7491 (mmm) REVERT: A 2461 MET cc_start: 0.8152 (mmp) cc_final: 0.7817 (mmp) REVERT: A 2510 MET cc_start: 0.8610 (tpp) cc_final: 0.8373 (tpp) REVERT: A 3008 MET cc_start: 0.9319 (mmm) cc_final: 0.9114 (tpp) REVERT: A 3030 MET cc_start: 0.8343 (mpp) cc_final: 0.7913 (mpp) REVERT: A 3068 MET cc_start: 0.8856 (ptp) cc_final: 0.8643 (ptp) REVERT: A 3500 MET cc_start: 0.7634 (tmm) cc_final: 0.7230 (tmm) REVERT: A 3524 MET cc_start: 0.7948 (tpp) cc_final: 0.7687 (tpp) REVERT: A 3791 MET cc_start: 0.8948 (ppp) cc_final: 0.8706 (ppp) REVERT: A 4128 MET cc_start: 0.7670 (pmm) cc_final: 0.6429 (pmm) REVERT: B 188 MET cc_start: 0.7574 (mmm) cc_final: 0.7310 (mmt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.3961 time to fit residues: 104.1991 Evaluate side-chains 132 residues out of total 3596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.781 ------------------------------------------------------------------------------- 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: 0.1980 chunk 338 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 318 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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** A2377 ASN A2468 ASN A2471 GLN ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.038943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.033209 restraints weight = 370726.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.033995 restraints weight = 206020.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.034125 restraints weight = 115826.197| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31095 Z= 0.183 Angle : 0.529 10.206 42310 Z= 0.266 Chirality : 0.039 0.156 4905 Planarity : 0.003 0.049 5441 Dihedral : 6.010 159.158 4366 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 1.47 (0.14), residues: 3987 helix: 2.27 (0.11), residues: 2112 sheet: -0.22 (0.23), residues: 484 loop : -0.60 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 177 HIS 0.003 0.001 HIS C 277 PHE 0.031 0.001 PHE A4147 TYR 0.027 0.001 TYR A3026 ARG 0.007 0.000 ARG A2684 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4719.81 seconds wall clock time: 89 minutes 9.85 seconds (5349.85 seconds total)