Starting phenix.real_space_refine on Thu May 29 18:00:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j2f_61095/05_2025/9j2f_61095.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j2f_61095/05_2025/9j2f_61095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j2f_61095/05_2025/9j2f_61095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j2f_61095/05_2025/9j2f_61095.map" model { file = "/net/cci-nas-00/data/ceres_data/9j2f_61095/05_2025/9j2f_61095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j2f_61095/05_2025/9j2f_61095.cif" } resolution = 2.2 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= 0.012 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: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 16 5.49 5 Mg 39 5.21 5 S 63 5.16 5 C 22544 2.51 5 N 4699 2.21 5 O 5552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32918 Number of models: 1 Model: "" Number of chains: 140 Chain: "C" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2585 Classifications: {'peptide': 331} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 299} Chain: "L" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2159 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "M" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2621 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 310} Chain: "H" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2041 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 239} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 407 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "G" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 232 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 24} Chain: "D" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "E" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 407 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "F" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "I" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "J" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 386 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "K" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "N" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "O" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 407 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "P" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "Q" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "R" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "S" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "T" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "U" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "V" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "W" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "X" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "Y" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "Z" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "1" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "2" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "3" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "4" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "5" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "6" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "7" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "8" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "9" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "0" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "a" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "b" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "c" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "d" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "e" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "f" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "g" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "h" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "i" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "j" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "k" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "l" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "m" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "n" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "o" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "p" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "q" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 424 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "r" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 400 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 188 Unusual residues: {' MG': 1, 'HEC': 4, 'UQ8': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UQ8:plan-4': 1, 'UQ8:plan-5': 1, 'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-2': 1, 'UQ8:plan-3': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1} Unresolved non-hydrogen planarities: 38 Chain: "L" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 326 Unusual residues: {'BCB': 2, 'BPB': 1, 'CDL': 1, 'DGA': 1, 'UQ8': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1, 'UQ8:plan-2': 1} Unresolved non-hydrogen planarities: 22 Chain: "M" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 519 Unusual residues: {' FE': 1, 'BCB': 2, 'BPB': 1, 'CDL': 1, 'LMT': 1, 'MQ7': 1, 'NS5': 1, 'PGV': 1, 'UQ8': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-2': 1, 'UQ8:plan-3': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 170 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 159 Unusual residues: {'BCB': 1, 'NS0': 1, 'UQ8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'BCB': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'BCB': 1, 'NS0': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 117 Unusual residues: {'BCB': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'BCB': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "O" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 115 Unusual residues: {'BCB': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'BCB': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 154 Unusual residues: {'BCB': 1, 'NS0': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "X" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'NS0': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'BCB': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 141 Unusual residues: {'BCB': 1, 'LMT': 1, 'NS0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 141 Unusual residues: {'BCB': 1, 'LMT': 1, 'NS0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "l" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCB': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 134 Unusual residues: {'BCB': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "L" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "M" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "U" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "4" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "5" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "6" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "7" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "9" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "e" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "f" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "n" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 21.19, per 1000 atoms: 0.64 Number of scatterers: 32918 At special positions: 0 Unit cell: (142.68, 145.96, 141.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 63 16.00 P 16 15.00 Mg 39 11.99 O 5552 8.00 N 4699 7.00 C 22544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=34, symmetry=0 Number of additional bonds: simple=34, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.23 Conformation dependent library (CDL) restraints added in 3.9 seconds 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 11 sheets defined 63.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'C' and resid 24 through 36 Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.874A pdb=" N VAL C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 81 Processing helix chain 'C' and resid 85 through 90 removed outlier: 4.203A pdb=" N THR C 88 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 121 removed outlier: 3.678A pdb=" N LYS C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 131 through 137 removed outlier: 4.332A pdb=" N CYS C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 169 through 176 Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 221 through 239 Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 247 through 251 removed outlier: 4.157A pdb=" N PHE C 251 " --> pdb=" O PRO C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 removed outlier: 3.592A pdb=" N LYS C 257 " --> pdb=" O TRP C 254 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 258 " --> pdb=" O GLY C 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 258' Processing helix chain 'C' and resid 259 through 279 removed outlier: 3.768A pdb=" N ALA C 263 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 287 Proline residue: C 285 - end of helix Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 302 through 308 removed outlier: 4.008A pdb=" N CYS C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'L' and resid 6 through 10 Processing helix chain 'L' and resid 31 through 55 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'L' and resid 83 through 111 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.825A pdb=" N VAL L 123 " --> pdb=" O ILE L 119 " (cutoff:3.500A) Proline residue: L 124 - end of helix Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 Processing helix chain 'L' and resid 151 through 163 Processing helix chain 'L' and resid 164 through 165 No H-bonds generated for 'chain 'L' and resid 164 through 165' Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 221 removed outlier: 3.540A pdb=" N PHE L 216 " --> pdb=" O GLU L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 251 removed outlier: 3.875A pdb=" N HIS L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE L 241 " --> pdb=" O ALA L 237 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE L 246 " --> pdb=" O LEU L 242 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY L 247 " --> pdb=" O THR L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 263 removed outlier: 3.675A pdb=" N TRP L 262 " --> pdb=" O GLY L 258 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 258 through 263' Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 269 through 273 Processing helix chain 'M' and resid 2 through 6 Processing helix chain 'M' and resid 25 through 27 No H-bonds generated for 'chain 'M' and resid 25 through 27' Processing helix chain 'M' and resid 38 through 43 removed outlier: 3.917A pdb=" N ILE M 42 " --> pdb=" O TRP M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 78 removed outlier: 3.504A pdb=" N VAL M 57 " --> pdb=" O GLY M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 89 Processing helix chain 'M' and resid 107 through 110 Processing helix chain 'M' and resid 111 through 139 Processing helix chain 'M' and resid 143 through 161 Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 169 through 173 removed outlier: 3.612A pdb=" N GLU M 172 " --> pdb=" O SER M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 192 removed outlier: 4.224A pdb=" N LEU M 182 " --> pdb=" O ILE M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 197 Processing helix chain 'M' and resid 198 through 225 Processing helix chain 'M' and resid 226 through 229 Processing helix chain 'M' and resid 232 through 239 Processing helix chain 'M' and resid 241 through 256 Processing helix chain 'M' and resid 262 through 286 removed outlier: 3.703A pdb=" N MET M 276 " --> pdb=" O SER M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 300 Processing helix chain 'M' and resid 322 through 326 Processing helix chain 'H' and resid 11 through 31 removed outlier: 3.578A pdb=" N TYR H 18 " --> pdb=" O GLN H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 37 Processing helix chain 'H' and resid 108 through 113 Processing helix chain 'H' and resid 114 through 118 Processing helix chain 'H' and resid 140 through 142 No H-bonds generated for 'chain 'H' and resid 140 through 142' Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'H' and resid 216 through 223 removed outlier: 3.548A pdb=" N ALA H 221 " --> pdb=" O SER H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 251 removed outlier: 3.688A pdb=" N TYR H 244 " --> pdb=" O VAL H 240 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU H 249 " --> pdb=" O ALA H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 257 Processing helix chain 'A' and resid 7 through 11 removed outlier: 4.548A pdb=" N TRP A 10 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 17 removed outlier: 4.183A pdb=" N ASP A 17 " --> pdb=" O TRP A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 42 Processing helix chain 'B' and resid 13 through 44 Processing helix chain 'G' and resid 14 through 16 No H-bonds generated for 'chain 'G' and resid 14 through 16' Processing helix chain 'G' and resid 17 through 35 Proline residue: G 27 - end of helix removed outlier: 3.526A pdb=" N TYR G 35 " --> pdb=" O ILE G 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 15 Processing helix chain 'D' and resid 17 through 43 removed outlier: 3.585A pdb=" N THR D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 44 Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 17 through 35 Proline residue: F 27 - end of helix removed outlier: 3.750A pdb=" N TYR F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 11 Processing helix chain 'I' and resid 12 through 17 removed outlier: 4.189A pdb=" N ASP I 17 " --> pdb=" O TRP I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 43 Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'K' and resid 17 through 36 Proline residue: K 27 - end of helix removed outlier: 3.526A pdb=" N TYR K 35 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG K 36 " --> pdb=" O ALA K 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 15 Processing helix chain 'N' and resid 17 through 42 Processing helix chain 'O' and resid 11 through 44 Processing helix chain 'P' and resid 17 through 35 Proline residue: P 27 - end of helix removed outlier: 3.524A pdb=" N TYR P 35 " --> pdb=" O ILE P 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 15 Processing helix chain 'Q' and resid 17 through 42 Processing helix chain 'R' and resid 11 through 44 Processing helix chain 'S' and resid 17 through 35 Proline residue: S 27 - end of helix removed outlier: 3.615A pdb=" N TYR S 35 " --> pdb=" O ILE S 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 15 Processing helix chain 'T' and resid 17 through 42 Processing helix chain 'U' and resid 13 through 44 Processing helix chain 'V' and resid 17 through 35 Proline residue: V 27 - end of helix Processing helix chain 'W' and resid 7 through 15 removed outlier: 4.374A pdb=" N TRP W 10 " --> pdb=" O SER W 7 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 42 Processing helix chain 'X' and resid 12 through 44 Processing helix chain 'Y' and resid 17 through 35 Proline residue: Y 27 - end of helix removed outlier: 3.663A pdb=" N TYR Y 35 " --> pdb=" O ILE Y 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 15 Processing helix chain 'Z' and resid 17 through 42 Processing helix chain '1' and resid 11 through 44 Processing helix chain '2' and resid 3 through 7 removed outlier: 3.880A pdb=" N SER 2 7 " --> pdb=" O ALA 2 4 " (cutoff:3.500A) Processing helix chain '2' and resid 14 through 16 No H-bonds generated for 'chain '2' and resid 14 through 16' Processing helix chain '2' and resid 17 through 35 Proline residue: 2 27 - end of helix removed outlier: 3.741A pdb=" N TYR 2 35 " --> pdb=" O ILE 2 31 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 15 Processing helix chain '3' and resid 17 through 42 Processing helix chain '4' and resid 11 through 44 Processing helix chain '5' and resid 17 through 35 Proline residue: 5 27 - end of helix removed outlier: 3.500A pdb=" N TYR 5 35 " --> pdb=" O ILE 5 31 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 15 Processing helix chain '6' and resid 17 through 43 Processing helix chain '7' and resid 11 through 44 Processing helix chain '8' and resid 17 through 35 Proline residue: 8 27 - end of helix removed outlier: 3.549A pdb=" N TYR 8 35 " --> pdb=" O ILE 8 31 " (cutoff:3.500A) Processing helix chain '9' and resid 8 through 15 Processing helix chain '9' and resid 17 through 42 Processing helix chain '0' and resid 11 through 44 Processing helix chain 'a' and resid 14 through 16 No H-bonds generated for 'chain 'a' and resid 14 through 16' Processing helix chain 'a' and resid 17 through 36 Proline residue: a 27 - end of helix removed outlier: 3.577A pdb=" N TYR a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 10 No H-bonds generated for 'chain 'b' and resid 8 through 10' Processing helix chain 'b' and resid 11 through 16 removed outlier: 3.776A pdb=" N ILE b 15 " --> pdb=" O LYS b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 41 Processing helix chain 'c' and resid 11 through 44 Processing helix chain 'd' and resid 17 through 35 Proline residue: d 27 - end of helix removed outlier: 3.567A pdb=" N TYR d 35 " --> pdb=" O ILE d 31 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 15 Processing helix chain 'e' and resid 17 through 43 removed outlier: 3.510A pdb=" N THR e 43 " --> pdb=" O GLY e 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 44 Processing helix chain 'g' and resid 14 through 16 No H-bonds generated for 'chain 'g' and resid 14 through 16' Processing helix chain 'g' and resid 17 through 35 Proline residue: g 27 - end of helix removed outlier: 3.620A pdb=" N TYR g 35 " --> pdb=" O ILE g 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 15 Processing helix chain 'h' and resid 17 through 42 Processing helix chain 'i' and resid 12 through 44 Processing helix chain 'j' and resid 17 through 35 Proline residue: j 27 - end of helix removed outlier: 3.622A pdb=" N TYR j 35 " --> pdb=" O ILE j 31 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 15 Processing helix chain 'k' and resid 17 through 42 Processing helix chain 'l' and resid 12 through 44 Processing helix chain 'm' and resid 17 through 35 Proline residue: m 27 - end of helix Processing helix chain 'n' and resid 7 through 15 removed outlier: 4.255A pdb=" N TRP n 10 " --> pdb=" O SER n 7 " (cutoff:3.500A) Processing helix chain 'n' and resid 17 through 42 Processing helix chain 'o' and resid 13 through 44 Processing helix chain 'p' and resid 17 through 36 Proline residue: p 27 - end of helix removed outlier: 3.508A pdb=" N ARG p 36 " --> pdb=" O ALA p 32 " (cutoff:3.500A) Processing helix chain 'q' and resid 8 through 15 Processing helix chain 'q' and resid 17 through 43 Processing helix chain 'r' and resid 11 through 44 Processing sheet with id=AA1, first strand: chain 'C' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'M' and resid 12 through 13 Processing sheet with id=AA4, first strand: chain 'M' and resid 29 through 30 Processing sheet with id=AA5, first strand: chain 'M' and resid 34 through 35 Processing sheet with id=AA6, first strand: chain 'M' and resid 93 through 94 Processing sheet with id=AA7, first strand: chain 'H' and resid 66 through 69 Processing sheet with id=AA8, first strand: chain 'H' and resid 92 through 94 Processing sheet with id=AA9, first strand: chain 'H' and resid 136 through 138 removed outlier: 5.619A pdb=" N VAL H 170 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER H 188 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP H 172 " --> pdb=" O GLU H 186 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP H 176 " --> pdb=" O PHE H 182 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N PHE H 182 " --> pdb=" O ASP H 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 136 through 138 removed outlier: 6.552A pdb=" N VAL H 159 " --> pdb=" O ALA H 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'j' and resid 2 through 3 1602 hydrogen bonds defined for protein. 4428 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: 9.81 Time building geometry restraints manager: 12.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 11617 1.38 - 1.56: 21825 1.56 - 1.75: 32 1.75 - 1.93: 115 1.93 - 2.11: 164 Bond restraints: 33753 Sorted by residual: bond pdb=" CA7 CDL H 302 " pdb=" OA8 CDL H 302 " ideal model delta sigma weight residual 1.334 1.458 -0.124 1.10e-02 8.26e+03 1.28e+02 bond pdb=" CA7 CDL H 301 " pdb=" OA8 CDL H 301 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.22e+02 bond pdb=" CAB HEC C 403 " pdb=" CBB HEC C 403 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAC HEC C 402 " pdb=" CBC HEC C 402 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAC HEC C 404 " pdb=" CBC HEC C 404 " ideal model delta sigma weight residual 1.544 1.326 0.218 2.00e-02 2.50e+03 1.19e+02 ... (remaining 33748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 43561 3.14 - 6.28: 2185 6.28 - 9.43: 507 9.43 - 12.57: 205 12.57 - 15.71: 57 Bond angle restraints: 46515 Sorted by residual: angle pdb=" C51 CDL r 102 " pdb=" CB5 CDL r 102 " pdb=" OB6 CDL r 102 " ideal model delta sigma weight residual 111.33 121.33 -10.00 1.32e+00 5.72e-01 5.72e+01 angle pdb=" C11 CDL H 301 " pdb=" CA5 CDL H 301 " pdb=" OA6 CDL H 301 " ideal model delta sigma weight residual 111.33 120.86 -9.53 1.32e+00 5.72e-01 5.19e+01 angle pdb=" C11 CDL H 302 " pdb=" CA5 CDL H 302 " pdb=" OA6 CDL H 302 " ideal model delta sigma weight residual 111.33 120.68 -9.35 1.32e+00 5.72e-01 5.00e+01 angle pdb=" C11 CDL M 409 " pdb=" CA5 CDL M 409 " pdb=" OA6 CDL M 409 " ideal model delta sigma weight residual 111.33 120.52 -9.19 1.32e+00 5.72e-01 4.84e+01 angle pdb=" C51 CDL M 409 " pdb=" CB5 CDL M 409 " pdb=" OB6 CDL M 409 " ideal model delta sigma weight residual 111.33 120.46 -9.13 1.32e+00 5.72e-01 4.77e+01 ... (remaining 46510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 17839 35.05 - 70.09: 717 70.09 - 105.14: 98 105.14 - 140.19: 31 140.19 - 175.24: 16 Dihedral angle restraints: 18701 sinusoidal: 8706 harmonic: 9995 Sorted by residual: dihedral pdb=" C1 BCB i 101 " pdb=" CGA BCB i 101 " pdb=" O2A BCB i 101 " pdb=" CBA BCB i 101 " ideal model delta sinusoidal sigma weight residual 180.00 24.51 155.49 1 6.00e+00 2.78e-02 5.09e+02 dihedral pdb=" CBD BCB 3 101 " pdb=" CGD BCB 3 101 " pdb=" O2D BCB 3 101 " pdb=" CED BCB 3 101 " ideal model delta sinusoidal sigma weight residual 180.00 -118.18 -61.82 1 5.00e+00 4.00e-02 2.03e+02 dihedral pdb=" CBD BCB h 102 " pdb=" CGD BCB h 102 " pdb=" O2D BCB h 102 " pdb=" CED BCB h 102 " ideal model delta sinusoidal sigma weight residual -180.00 -120.78 -59.22 1 5.00e+00 4.00e-02 1.88e+02 ... (remaining 18698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4053 0.074 - 0.148: 610 0.148 - 0.223: 89 0.223 - 0.297: 55 0.297 - 0.371: 6 Chirality restraints: 4813 Sorted by residual: chirality pdb=" C02 PGV N 102 " pdb=" C01 PGV N 102 " pdb=" C03 PGV N 102 " pdb=" O01 PGV N 102 " both_signs ideal model delta sigma weight residual False 2.36 2.73 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" C2C BCB M 403 " pdb=" C1C BCB M 403 " pdb=" C3C BCB M 403 " pdb=" CMC BCB M 403 " both_signs ideal model delta sigma weight residual False -2.62 -2.98 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C2C BCB M 402 " pdb=" C1C BCB M 402 " pdb=" C3C BCB M 402 " pdb=" CMC BCB M 402 " both_signs ideal model delta sigma weight residual False -2.62 -2.96 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 4810 not shown) Planarity restraints: 5557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCB A 102 " -0.289 3.00e-02 1.11e+03 2.33e-01 3.01e+02 pdb=" CBA BCB A 102 " -0.185 3.00e-02 1.11e+03 pdb=" CGA BCB A 102 " 0.071 3.00e-02 1.11e+03 pdb=" O1A BCB A 102 " 0.018 3.00e-02 1.11e+03 pdb=" O2A BCB A 102 " 0.384 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C31 NS0 O 101 " -0.167 2.00e-02 2.50e+03 1.40e-01 2.45e+02 pdb=" C32 NS0 O 101 " 0.225 2.00e-02 2.50e+03 pdb=" C33 NS0 O 101 " 0.056 2.00e-02 2.50e+03 pdb=" C34 NS0 O 101 " 0.014 2.00e-02 2.50e+03 pdb=" C35 NS0 O 101 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCB 9 101 " -0.255 3.00e-02 1.11e+03 2.04e-01 2.32e+02 pdb=" CBA BCB 9 101 " -0.170 3.00e-02 1.11e+03 pdb=" CGA BCB 9 101 " 0.062 3.00e-02 1.11e+03 pdb=" O1A BCB 9 101 " 0.031 3.00e-02 1.11e+03 pdb=" O2A BCB 9 101 " 0.332 3.00e-02 1.11e+03 ... (remaining 5554 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 328 2.60 - 3.17: 27626 3.17 - 3.75: 57444 3.75 - 4.32: 83735 4.32 - 4.90: 131292 Nonbonded interactions: 300425 Sorted by model distance: nonbonded pdb=" NE2 HIS C 124 " pdb="FE HEC C 404 " model vdw 2.020 3.080 nonbonded pdb=" OE2 GLU M 233 " pdb="FE FE M 401 " model vdw 2.066 2.260 nonbonded pdb="MG MG C 405 " pdb=" O HOH b 205 " model vdw 2.074 2.170 nonbonded pdb="MG MG C 405 " pdb=" O HOH 9 205 " model vdw 2.095 2.170 nonbonded pdb="MG MG C 405 " pdb=" O HOH C 525 " model vdw 2.106 2.170 ... (remaining 300420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 8 through 55) selection = (chain '1' and resid 8 through 55) selection = (chain '4' and resid 8 through 55) selection = (chain '7' and resid 8 through 55) selection = (chain 'B' and resid 8 through 55) selection = (chain 'E' and resid 8 through 55) selection = (chain 'J' and resid 8 through 55) selection = (chain 'O' and resid 8 through 55) selection = (chain 'R' and resid 8 through 55) selection = (chain 'U' and resid 8 through 55) selection = (chain 'X' and resid 8 through 55) selection = (chain 'c' and resid 8 through 55) selection = (chain 'f' and resid 8 through 55) selection = (chain 'i' and resid 8 through 55) selection = (chain 'l' and resid 8 through 55) selection = (chain 'o' and resid 8 through 55) selection = (chain 'r' and resid 8 through 55) } ncs_group { reference = (chain '2' and resid 1 through 36) selection = chain '5' selection = chain '8' selection = chain 'F' selection = chain 'K' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'j' selection = chain 'm' selection = chain 'p' } ncs_group { reference = (chain '3' and resid 7 through 56) selection = (chain '6' and resid 7 through 56) selection = (chain '9' and resid 7 through 56) selection = (chain 'A' and resid 7 through 56) selection = (chain 'D' and resid 7 through 56) selection = (chain 'I' and resid 7 through 56) selection = (chain 'N' and resid 7 through 56) selection = (chain 'Q' and resid 7 through 56) selection = (chain 'T' and resid 7 through 56) selection = (chain 'W' and resid 7 through 56) selection = (chain 'Z' and resid 7 through 56) selection = (chain 'b' and resid 7 through 56) selection = (chain 'e' and resid 7 through 56) selection = (chain 'h' and resid 7 through 56) selection = (chain 'k' and resid 7 through 56) selection = (chain 'n' and resid 7 through 56) selection = (chain 'q' and resid 7 through 56) } 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 individual isotropic 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.340 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 72.560 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.380 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:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 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 : 0.018 0.344 33787 Z= 0.873 Angle : 1.689 15.709 46515 Z= 0.757 Chirality : 0.060 0.371 4813 Planarity : 0.015 0.233 5557 Dihedral : 19.250 175.237 12245 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.82 % Allowed : 4.15 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.53 (0.14), residues: 3355 helix: 1.52 (0.12), residues: 1813 sheet: -1.05 (0.77), residues: 32 loop : 0.59 (0.17), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP Y 30 HIS 0.012 0.002 HIS M 181 PHE 0.024 0.003 PHE C 188 TYR 0.023 0.003 TYR L 164 ARG 0.005 0.001 ARG q 45 Details of bonding type rmsd hydrogen bonds : bond 0.15409 ( 1600) hydrogen bonds : angle 6.67921 ( 4428) covalent geometry : bond 0.01760 (33753) covalent geometry : angle 1.68909 (46515) Misc. bond : bond 0.13368 ( 34) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 3.397 Fit side-chains REVERT: C 50 GLN cc_start: 0.6440 (pt0) cc_final: 0.6048 (mt0) REVERT: C 95 ASP cc_start: 0.7663 (t0) cc_final: 0.7435 (t70) REVERT: C 127 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8249 (mp10) REVERT: M 32 LYS cc_start: 0.8345 (tppp) cc_final: 0.7988 (ttmt) REVERT: H 51 LYS cc_start: 0.7946 (ptmt) cc_final: 0.7204 (ptpt) REVERT: H 108 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7418 (t0) REVERT: H 121 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6434 (pt0) REVERT: H 194 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6884 (tmt90) REVERT: H 225 ARG cc_start: 0.8327 (mtt90) cc_final: 0.8123 (mtt-85) REVERT: B 7 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6138 (pt) REVERT: B 22 PHE cc_start: 0.8113 (t80) cc_final: 0.7835 (t80) REVERT: D 53 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7965 (ptt-90) REVERT: E 12 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: E 13 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7339 (mp0) REVERT: I 17 ASP cc_start: 0.8063 (t0) cc_final: 0.7649 (t0) REVERT: K 2 PHE cc_start: 0.7894 (m-80) cc_final: 0.7693 (m-80) REVERT: R 14 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7400 (mt-10) REVERT: T 19 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6489 (ttm110) REVERT: T 53 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8005 (mpp80) REVERT: W 17 ASP cc_start: 0.7241 (t0) cc_final: 0.6800 (t0) REVERT: W 20 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7730 (mtp85) REVERT: W 35 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8982 (mp) REVERT: X 52 LYS cc_start: 0.8200 (tttp) cc_final: 0.7851 (tppt) REVERT: 6 17 ASP cc_start: 0.7713 (t0) cc_final: 0.7442 (t0) REVERT: 6 53 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7000 (ptt-90) REVERT: 7 12 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6963 (mt-10) REVERT: 9 19 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7845 (mtm-85) REVERT: 0 16 LYS cc_start: 0.8331 (mttp) cc_final: 0.8097 (mttp) REVERT: d 33 LEU cc_start: 0.8516 (mt) cc_final: 0.8188 (mt) REVERT: d 34 LEU cc_start: 0.8567 (tp) cc_final: 0.8362 (tm) REVERT: e 17 ASP cc_start: 0.7787 (t0) cc_final: 0.7527 (t0) REVERT: j 12 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7887 (pp) REVERT: k 20 ARG cc_start: 0.8174 (ttt90) cc_final: 0.7948 (ttt90) REVERT: o 13 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6706 (mt-10) REVERT: o 26 MET cc_start: 0.8954 (ttp) cc_final: 0.8745 (ttp) REVERT: r 26 MET cc_start: 0.8462 (ttp) cc_final: 0.8102 (ttt) outliers start: 53 outliers final: 21 residues processed: 386 average time/residue: 1.6303 time to fit residues: 736.6872 Evaluate side-chains 338 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 305 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain M residue 17 HIS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain T residue 19 ARG Chi-restraints excluded: chain T residue 53 ARG Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain l residue 10 LEU Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain q residue 16 LEU Chi-restraints excluded: chain r residue 27 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 262 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 304 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 184 ASN C 267 GLN C 295 GLN H 108 ASN H 222 ASN D 44 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.095764 restraints weight = 31894.325| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 0.95 r_work: 0.2847 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.458 33787 Z= 0.233 Angle : 0.897 13.820 46515 Z= 0.397 Chirality : 0.048 0.196 4813 Planarity : 0.006 0.060 5557 Dihedral : 21.080 178.117 6239 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.72 % Allowed : 5.93 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3355 helix: 1.39 (0.12), residues: 1907 sheet: -0.68 (0.79), residues: 32 loop : 0.10 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP 2 18 HIS 0.010 0.002 HIS M 181 PHE 0.029 0.002 PHE C 188 TYR 0.023 0.003 TYR C 225 ARG 0.011 0.001 ARG 2 36 Details of bonding type rmsd hydrogen bonds : bond 0.07068 ( 1600) hydrogen bonds : angle 5.30943 ( 4428) covalent geometry : bond 0.00545 (33753) covalent geometry : angle 0.89680 (46515) Misc. bond : bond 0.11106 ( 34) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 312 time to evaluate : 3.873 Fit side-chains REVERT: C 46 LYS cc_start: 0.6654 (pmtt) cc_final: 0.6176 (ttmt) REVERT: C 50 GLN cc_start: 0.6302 (pt0) cc_final: 0.5917 (mt0) REVERT: C 95 ASP cc_start: 0.7820 (t0) cc_final: 0.7446 (t70) REVERT: C 127 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8132 (mp-120) REVERT: C 256 ASN cc_start: 0.8486 (p0) cc_final: 0.8232 (p0) REVERT: L 72 LYS cc_start: 0.8849 (pttp) cc_final: 0.8619 (pttm) REVERT: M 32 LYS cc_start: 0.8272 (tppp) cc_final: 0.7923 (ttmt) REVERT: M 215 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.8945 (t80) REVERT: H 51 LYS cc_start: 0.7918 (ptmt) cc_final: 0.7159 (ptpt) REVERT: H 121 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6309 (pt0) REVERT: H 194 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6820 (tmt90) REVERT: B 7 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6066 (pt) REVERT: B 22 PHE cc_start: 0.8074 (t80) cc_final: 0.7782 (t80) REVERT: E 12 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: E 13 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7226 (mp0) REVERT: J 14 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: R 14 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7271 (mt-10) REVERT: T 53 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8133 (mpp80) REVERT: W 17 ASP cc_start: 0.7019 (t0) cc_final: 0.6615 (t70) REVERT: W 20 ARG cc_start: 0.7974 (mtt-85) cc_final: 0.7770 (mtp85) REVERT: W 35 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8967 (mp) REVERT: X 52 LYS cc_start: 0.8160 (tttp) cc_final: 0.7845 (tppt) REVERT: 0 16 LYS cc_start: 0.8273 (mttp) cc_final: 0.8028 (mttp) REVERT: d 34 LEU cc_start: 0.8678 (tp) cc_final: 0.8422 (tm) REVERT: e 17 ASP cc_start: 0.7650 (t0) cc_final: 0.7400 (t0) REVERT: h 53 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6881 (mtp85) REVERT: j 12 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7884 (pp) REVERT: k 20 ARG cc_start: 0.8056 (ttt90) cc_final: 0.7784 (ttt90) REVERT: o 13 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6546 (mt-10) REVERT: r 26 MET cc_start: 0.8417 (ttp) cc_final: 0.8056 (ttt) outliers start: 50 outliers final: 29 residues processed: 351 average time/residue: 1.6396 time to fit residues: 673.3807 Evaluate side-chains 335 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 17 HIS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain T residue 53 ARG Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 53 ARG Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain l residue 10 LEU Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain q residue 16 LEU Chi-restraints excluded: chain r residue 27 VAL Chi-restraints excluded: chain r residue 50 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 293 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 281 optimal weight: 0.9980 chunk 334 optimal weight: 0.1980 chunk 219 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 295 GLN H 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.100139 restraints weight = 32470.917| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 0.95 r_work: 0.2920 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.355 33787 Z= 0.150 Angle : 0.737 13.157 46515 Z= 0.321 Chirality : 0.042 0.172 4813 Planarity : 0.004 0.045 5557 Dihedral : 19.611 174.530 6225 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.54 % Allowed : 6.72 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.57 (0.14), residues: 3355 helix: 1.57 (0.12), residues: 1937 sheet: -0.55 (0.83), residues: 32 loop : 0.46 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP V 30 HIS 0.008 0.001 HIS M 181 PHE 0.023 0.002 PHE L 146 TYR 0.019 0.002 TYR C 225 ARG 0.005 0.000 ARG 9 19 Details of bonding type rmsd hydrogen bonds : bond 0.05627 ( 1600) hydrogen bonds : angle 4.93330 ( 4428) covalent geometry : bond 0.00342 (33753) covalent geometry : angle 0.73724 (46515) Misc. bond : bond 0.09615 ( 34) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 334 time to evaluate : 3.422 Fit side-chains REVERT: C 46 LYS cc_start: 0.6428 (pmtt) cc_final: 0.5946 (tttp) REVERT: C 95 ASP cc_start: 0.7839 (t0) cc_final: 0.7429 (t70) REVERT: C 127 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8073 (mp-120) REVERT: C 256 ASN cc_start: 0.8479 (p0) cc_final: 0.8242 (p0) REVERT: M 32 LYS cc_start: 0.8304 (tppp) cc_final: 0.7932 (ttmt) REVERT: M 215 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8865 (t80) REVERT: H 51 LYS cc_start: 0.7919 (ptmt) cc_final: 0.7142 (ptpt) REVERT: H 121 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6259 (pt0) REVERT: B 7 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6061 (pt) REVERT: B 22 PHE cc_start: 0.8081 (t80) cc_final: 0.7789 (t80) REVERT: E 12 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: E 13 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7197 (mp0) REVERT: J 14 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: R 14 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7163 (mt-10) REVERT: U 12 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5910 (tp30) REVERT: W 17 ASP cc_start: 0.6915 (t0) cc_final: 0.6572 (t70) REVERT: W 20 ARG cc_start: 0.7911 (mtt-85) cc_final: 0.7704 (mtp85) REVERT: W 35 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8933 (mp) REVERT: X 12 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6054 (tp30) REVERT: X 52 LYS cc_start: 0.8150 (tttp) cc_final: 0.7827 (tppt) REVERT: 6 53 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6952 (ptt-90) REVERT: 7 12 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6828 (mt-10) REVERT: 0 14 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6813 (mm-30) REVERT: 0 16 LYS cc_start: 0.8283 (mttp) cc_final: 0.8034 (mttm) REVERT: d 34 LEU cc_start: 0.8633 (tp) cc_final: 0.8271 (tm) REVERT: e 53 ARG cc_start: 0.8565 (mtm180) cc_final: 0.8263 (mtm180) REVERT: f 17 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7822 (mt-10) REVERT: i 12 GLU cc_start: 0.6407 (tp30) cc_final: 0.6080 (tp30) REVERT: j 12 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7828 (pp) REVERT: k 19 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7950 (mtm-85) REVERT: n 20 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7608 (ttm110) REVERT: o 13 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6570 (mt-10) REVERT: r 26 MET cc_start: 0.8371 (ttp) cc_final: 0.8006 (ttt) outliers start: 45 outliers final: 24 residues processed: 368 average time/residue: 1.5570 time to fit residues: 677.1617 Evaluate side-chains 338 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 12 GLU Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain m residue 5 ASP Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 20 ARG Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain q residue 16 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 219 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 157 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 307 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 130 optimal weight: 0.0970 chunk 98 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 295 GLN M 17 HIS H 82 ASN H 222 ASN q 44 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.098595 restraints weight = 32214.704| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 0.92 r_work: 0.2849 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.349 33787 Z= 0.173 Angle : 0.782 14.254 46515 Z= 0.343 Chirality : 0.043 0.180 4813 Planarity : 0.005 0.045 5557 Dihedral : 19.465 173.021 6211 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.75 % Allowed : 7.14 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.54 (0.14), residues: 3355 helix: 1.52 (0.12), residues: 1937 sheet: -0.12 (1.17), residues: 20 loop : 0.48 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP d 30 HIS 0.009 0.001 HIS M 17 PHE 0.024 0.002 PHE L 146 TYR 0.021 0.002 TYR C 225 ARG 0.004 0.000 ARG 9 19 Details of bonding type rmsd hydrogen bonds : bond 0.06030 ( 1600) hydrogen bonds : angle 5.00339 ( 4428) covalent geometry : bond 0.00399 (33753) covalent geometry : angle 0.78200 (46515) Misc. bond : bond 0.09802 ( 34) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 310 time to evaluate : 3.483 Fit side-chains REVERT: C 46 LYS cc_start: 0.6524 (pmtt) cc_final: 0.6040 (tttp) REVERT: C 74 MET cc_start: 0.8972 (mmt) cc_final: 0.8530 (mmt) REVERT: C 95 ASP cc_start: 0.7839 (t0) cc_final: 0.7444 (t70) REVERT: C 110 MET cc_start: 0.9191 (mmt) cc_final: 0.8972 (mmt) REVERT: C 127 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8148 (mp-120) REVERT: C 256 ASN cc_start: 0.8565 (p0) cc_final: 0.8341 (p0) REVERT: L 139 MET cc_start: 0.9316 (mmm) cc_final: 0.9115 (mmm) REVERT: M 32 LYS cc_start: 0.8339 (tppp) cc_final: 0.7944 (ttmt) REVERT: M 215 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8951 (t80) REVERT: H 51 LYS cc_start: 0.7958 (ptmt) cc_final: 0.7180 (ptpt) REVERT: H 121 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6342 (pt0) REVERT: B 7 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6019 (pt) REVERT: B 22 PHE cc_start: 0.8085 (t80) cc_final: 0.7779 (t80) REVERT: E 13 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7275 (mp0) REVERT: J 14 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: R 14 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7212 (mt-10) REVERT: W 17 ASP cc_start: 0.7063 (t0) cc_final: 0.6695 (t70) REVERT: W 20 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7678 (mtp85) REVERT: W 35 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8908 (mp) REVERT: X 12 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6106 (tp30) REVERT: X 52 LYS cc_start: 0.8194 (tttp) cc_final: 0.7847 (tppt) REVERT: 6 53 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6975 (ptt-90) REVERT: 7 12 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: 0 14 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6827 (mm-30) REVERT: 0 16 LYS cc_start: 0.8323 (mttp) cc_final: 0.8074 (mttm) REVERT: d 34 LEU cc_start: 0.8641 (tp) cc_final: 0.8215 (tm) REVERT: e 53 ARG cc_start: 0.8601 (mtm180) cc_final: 0.8304 (mtm180) REVERT: i 12 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5764 (mp0) REVERT: j 12 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7842 (pp) REVERT: n 20 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7660 (ttm110) REVERT: o 13 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6642 (mt-10) REVERT: r 26 MET cc_start: 0.8419 (ttp) cc_final: 0.8050 (ttt) outliers start: 51 outliers final: 28 residues processed: 345 average time/residue: 1.6407 time to fit residues: 666.1556 Evaluate side-chains 337 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 17 HIS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain i residue 12 GLU Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain l residue 10 LEU Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 20 ARG Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain q residue 16 LEU Chi-restraints excluded: chain r residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 265 optimal weight: 0.0670 chunk 183 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 295 GLN M 17 HIS H 82 ASN H 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.123926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.097554 restraints weight = 32006.163| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 0.95 r_work: 0.2877 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.357 33787 Z= 0.185 Angle : 0.799 14.290 46515 Z= 0.351 Chirality : 0.044 0.183 4813 Planarity : 0.005 0.046 5557 Dihedral : 19.458 176.433 6206 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.89 % Allowed : 7.34 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.51 (0.14), residues: 3355 helix: 1.48 (0.12), residues: 1937 sheet: -0.07 (1.15), residues: 20 loop : 0.49 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP d 30 HIS 0.015 0.002 HIS M 17 PHE 0.025 0.002 PHE L 146 TYR 0.020 0.002 TYR C 225 ARG 0.005 0.001 ARG 9 19 Details of bonding type rmsd hydrogen bonds : bond 0.06163 ( 1600) hydrogen bonds : angle 5.03313 ( 4428) covalent geometry : bond 0.00429 (33753) covalent geometry : angle 0.79859 (46515) Misc. bond : bond 0.09805 ( 34) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 306 time to evaluate : 3.447 Fit side-chains REVERT: C 46 LYS cc_start: 0.6522 (pmtt) cc_final: 0.6077 (tttp) REVERT: C 74 MET cc_start: 0.8941 (mmt) cc_final: 0.8542 (mmt) REVERT: C 95 ASP cc_start: 0.7816 (t0) cc_final: 0.7420 (t70) REVERT: C 127 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8114 (mp-120) REVERT: C 256 ASN cc_start: 0.8514 (p0) cc_final: 0.8261 (p0) REVERT: M 32 LYS cc_start: 0.8304 (tppp) cc_final: 0.7909 (ttmt) REVERT: M 215 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.8964 (t80) REVERT: H 51 LYS cc_start: 0.7950 (ptmt) cc_final: 0.7172 (ptpt) REVERT: H 121 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6325 (pt0) REVERT: H 131 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: H 194 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6803 (tmt90) REVERT: B 7 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6007 (pt) REVERT: B 17 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6477 (tp30) REVERT: B 22 PHE cc_start: 0.8060 (t80) cc_final: 0.7757 (t80) REVERT: E 13 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7226 (mp0) REVERT: J 14 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: W 17 ASP cc_start: 0.7032 (t0) cc_final: 0.6570 (t70) REVERT: W 20 ARG cc_start: 0.7889 (mtt-85) cc_final: 0.7532 (mtp85) REVERT: W 35 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8891 (mp) REVERT: X 12 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6066 (tp30) REVERT: X 17 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6940 (tt0) REVERT: X 52 LYS cc_start: 0.8171 (tttp) cc_final: 0.7835 (tppt) REVERT: 2 33 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8007 (mp) REVERT: 6 53 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6924 (ptt-90) REVERT: 7 12 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6849 (mt-10) REVERT: 0 14 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6782 (mm-30) REVERT: 0 16 LYS cc_start: 0.8293 (mttp) cc_final: 0.8040 (mttp) REVERT: e 53 ARG cc_start: 0.8564 (mtm180) cc_final: 0.8272 (mtm180) REVERT: i 12 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5779 (mp0) REVERT: j 12 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7820 (pp) REVERT: n 20 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7601 (ttm110) REVERT: o 13 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6530 (mt-10) REVERT: r 26 MET cc_start: 0.8406 (ttp) cc_final: 0.8038 (ttt) outliers start: 55 outliers final: 31 residues processed: 347 average time/residue: 1.6472 time to fit residues: 673.0512 Evaluate side-chains 343 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain Y residue 5 ASP Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain i residue 12 GLU Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain l residue 10 LEU Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 20 ARG Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain q residue 16 LEU Chi-restraints excluded: chain r residue 50 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 128 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 chunk 305 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 311 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 295 GLN M 17 HIS H 82 ASN H 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.101282 restraints weight = 32307.112| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 0.87 r_work: 0.2885 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.326 33787 Z= 0.154 Angle : 0.734 13.275 46515 Z= 0.322 Chirality : 0.042 0.173 4813 Planarity : 0.004 0.045 5557 Dihedral : 19.060 175.479 6206 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.96 % Allowed : 7.55 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.62 (0.14), residues: 3355 helix: 1.60 (0.12), residues: 1934 sheet: -0.00 (1.17), residues: 20 loop : 0.50 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP d 30 HIS 0.009 0.001 HIS M 17 PHE 0.024 0.002 PHE L 146 TYR 0.019 0.002 TYR C 225 ARG 0.007 0.000 ARG 9 19 Details of bonding type rmsd hydrogen bonds : bond 0.05596 ( 1600) hydrogen bonds : angle 4.88071 ( 4428) covalent geometry : bond 0.00352 (33753) covalent geometry : angle 0.73382 (46515) Misc. bond : bond 0.09156 ( 34) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 315 time to evaluate : 3.219 Fit side-chains REVERT: C 46 LYS cc_start: 0.6434 (pmtt) cc_final: 0.5971 (tttp) REVERT: C 74 MET cc_start: 0.8931 (mmt) cc_final: 0.8495 (mmt) REVERT: C 95 ASP cc_start: 0.7817 (t0) cc_final: 0.7407 (t70) REVERT: C 127 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8094 (mp-120) REVERT: C 256 ASN cc_start: 0.8519 (p0) cc_final: 0.8287 (p0) REVERT: M 32 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7926 (ttmt) REVERT: M 215 PHE cc_start: 0.9337 (OUTLIER) cc_final: 0.8892 (t80) REVERT: H 51 LYS cc_start: 0.7941 (ptmt) cc_final: 0.7152 (ptpt) REVERT: H 121 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6239 (pt0) REVERT: H 194 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6776 (tmt90) REVERT: H 254 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: B 7 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6047 (pt) REVERT: B 22 PHE cc_start: 0.8094 (t80) cc_final: 0.7799 (t80) REVERT: E 13 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7266 (mp0) REVERT: J 14 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: U 12 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.6125 (tm-30) REVERT: W 17 ASP cc_start: 0.7104 (t0) cc_final: 0.6708 (t70) REVERT: W 20 ARG cc_start: 0.7837 (mtt-85) cc_final: 0.7504 (mtp85) REVERT: W 35 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8930 (mp) REVERT: X 12 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6064 (tp30) REVERT: X 17 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6937 (tt0) REVERT: X 52 LYS cc_start: 0.8193 (tttp) cc_final: 0.7850 (tppt) REVERT: 2 33 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8013 (mp) REVERT: 6 53 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6970 (ptt-90) REVERT: 7 12 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: 0 14 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6813 (mm-30) REVERT: 0 16 LYS cc_start: 0.8320 (mttp) cc_final: 0.8062 (mttm) REVERT: e 53 ARG cc_start: 0.8593 (mtm180) cc_final: 0.8321 (mtm180) REVERT: i 12 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5710 (mp0) REVERT: j 12 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7823 (pp) REVERT: o 13 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6594 (mt-10) REVERT: r 26 MET cc_start: 0.8370 (ttp) cc_final: 0.8009 (ttt) outliers start: 57 outliers final: 29 residues processed: 352 average time/residue: 1.5678 time to fit residues: 648.2318 Evaluate side-chains 344 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain U residue 12 GLU Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain Y residue 5 ASP Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain i residue 12 GLU Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain q residue 16 LEU Chi-restraints excluded: chain r residue 50 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 75 optimal weight: 0.9990 chunk 165 optimal weight: 0.0270 chunk 264 optimal weight: 5.9990 chunk 256 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 305 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 330 optimal weight: 20.0000 chunk 303 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 overall best weight: 0.8844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 295 GLN M 17 HIS H 82 ASN H 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.101983 restraints weight = 32235.833| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 0.96 r_work: 0.2952 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.284 33787 Z= 0.133 Angle : 0.684 12.156 46515 Z= 0.298 Chirality : 0.041 0.167 4813 Planarity : 0.004 0.045 5557 Dihedral : 18.488 177.993 6206 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.75 % Allowed : 7.86 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.77 (0.15), residues: 3355 helix: 1.70 (0.12), residues: 1941 sheet: 0.02 (1.16), residues: 20 loop : 0.58 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 5 30 HIS 0.009 0.001 HIS M 17 PHE 0.022 0.001 PHE L 146 TYR 0.019 0.002 TYR j 1 ARG 0.008 0.000 ARG 9 19 Details of bonding type rmsd hydrogen bonds : bond 0.05047 ( 1600) hydrogen bonds : angle 4.70921 ( 4428) covalent geometry : bond 0.00302 (33753) covalent geometry : angle 0.68392 (46515) Misc. bond : bond 0.08305 ( 34) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 324 time to evaluate : 3.411 Fit side-chains REVERT: C 46 LYS cc_start: 0.6417 (pmtt) cc_final: 0.5969 (tttp) REVERT: C 95 ASP cc_start: 0.7812 (t0) cc_final: 0.7403 (t70) REVERT: C 127 GLN cc_start: 0.8486 (mm-40) cc_final: 0.7942 (mp10) REVERT: C 256 ASN cc_start: 0.8460 (p0) cc_final: 0.8214 (p0) REVERT: M 32 LYS cc_start: 0.8321 (tppp) cc_final: 0.7908 (ttmt) REVERT: H 51 LYS cc_start: 0.7910 (ptmt) cc_final: 0.7115 (ptpt) REVERT: H 121 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6208 (pt0) REVERT: B 7 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6028 (pt) REVERT: B 17 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6442 (tp30) REVERT: B 22 PHE cc_start: 0.8050 (t80) cc_final: 0.7761 (t80) REVERT: E 13 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7182 (mp0) REVERT: J 14 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: T 20 ARG cc_start: 0.7142 (mtm110) cc_final: 0.6740 (mtm110) REVERT: W 17 ASP cc_start: 0.7008 (t0) cc_final: 0.6634 (t70) REVERT: 1 14 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7862 (pt0) REVERT: 2 33 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8070 (mp) REVERT: 6 53 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6999 (ptt-90) REVERT: 7 12 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6841 (mt-10) REVERT: 0 14 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6800 (mm-30) REVERT: 0 16 LYS cc_start: 0.8301 (mttp) cc_final: 0.8032 (mttp) REVERT: e 53 ARG cc_start: 0.8530 (mtm180) cc_final: 0.8271 (mtm180) REVERT: f 17 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7988 (mt-10) REVERT: i 12 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5635 (mp0) REVERT: j 12 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7821 (pp) REVERT: p 18 TRP cc_start: 0.7673 (m100) cc_final: 0.7466 (m100) outliers start: 51 outliers final: 25 residues processed: 356 average time/residue: 1.5786 time to fit residues: 662.7165 Evaluate side-chains 335 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 302 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain X residue 26 MET Chi-restraints excluded: chain Y residue 5 ASP Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain i residue 12 GLU Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain q residue 16 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 63 optimal weight: 7.9990 chunk 204 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 267 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 329 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 232 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 295 GLN M 17 HIS H 82 ASN H 222 ASN q 44 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.100012 restraints weight = 32156.061| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 0.86 r_work: 0.2859 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.373 33787 Z= 0.194 Angle : 0.814 14.073 46515 Z= 0.357 Chirality : 0.045 0.186 4813 Planarity : 0.005 0.056 5557 Dihedral : 19.093 178.320 6201 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.44 % Allowed : 8.71 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.59 (0.14), residues: 3355 helix: 1.53 (0.12), residues: 1934 sheet: 0.07 (1.15), residues: 20 loop : 0.57 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP d 30 HIS 0.011 0.002 HIS C 124 PHE 0.024 0.002 PHE L 146 TYR 0.021 0.002 TYR C 225 ARG 0.010 0.001 ARG 9 19 Details of bonding type rmsd hydrogen bonds : bond 0.06258 ( 1600) hydrogen bonds : angle 5.03608 ( 4428) covalent geometry : bond 0.00452 (33753) covalent geometry : angle 0.81383 (46515) Misc. bond : bond 0.10267 ( 34) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 307 time to evaluate : 3.944 Fit side-chains REVERT: C 46 LYS cc_start: 0.6544 (pmtt) cc_final: 0.6071 (tttp) REVERT: C 95 ASP cc_start: 0.7805 (t0) cc_final: 0.7416 (t70) REVERT: C 127 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8137 (mp-120) REVERT: C 256 ASN cc_start: 0.8497 (p0) cc_final: 0.8263 (p0) REVERT: M 7 TYR cc_start: 0.9123 (p90) cc_final: 0.8907 (p90) REVERT: M 17 HIS cc_start: 0.6233 (OUTLIER) cc_final: 0.6030 (p90) REVERT: M 32 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7922 (ttmt) REVERT: H 51 LYS cc_start: 0.7955 (ptmt) cc_final: 0.7187 (ptpt) REVERT: H 121 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6280 (pt0) REVERT: B 7 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6087 (pt) REVERT: B 17 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6508 (tp30) REVERT: B 22 PHE cc_start: 0.8082 (t80) cc_final: 0.7793 (t80) REVERT: D 53 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7962 (ptt-90) REVERT: E 13 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7295 (mp0) REVERT: I 20 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7645 (ttm110) REVERT: J 14 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: W 17 ASP cc_start: 0.7123 (t0) cc_final: 0.6834 (t70) REVERT: X 12 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6048 (tp30) REVERT: X 17 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6928 (mt-10) REVERT: 2 33 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8005 (mp) REVERT: 6 53 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6995 (ptt-90) REVERT: 7 12 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6869 (mt-10) REVERT: 0 14 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6839 (mm-30) REVERT: 0 16 LYS cc_start: 0.8277 (mttp) cc_final: 0.8016 (mttm) REVERT: e 53 ARG cc_start: 0.8588 (mtm180) cc_final: 0.8315 (mtm180) REVERT: j 12 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7833 (pp) REVERT: p 18 TRP cc_start: 0.7846 (m100) cc_final: 0.7637 (m100) outliers start: 42 outliers final: 25 residues processed: 337 average time/residue: 1.7130 time to fit residues: 675.1597 Evaluate side-chains 331 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 295 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 17 HIS Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain X residue 26 MET Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain q residue 16 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 279 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 290 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 295 GLN M 17 HIS H 82 ASN H 222 ASN ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.098158 restraints weight = 31928.402| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 0.95 r_work: 0.2889 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.370 33787 Z= 0.165 Angle : 0.762 13.502 46515 Z= 0.333 Chirality : 0.043 0.178 4813 Planarity : 0.005 0.046 5557 Dihedral : 18.922 176.663 6201 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.44 % Allowed : 9.02 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.62 (0.14), residues: 3355 helix: 1.55 (0.12), residues: 1934 sheet: 0.10 (1.17), residues: 20 loop : 0.57 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP d 30 HIS 0.022 0.001 HIS M 17 PHE 0.024 0.002 PHE L 146 TYR 0.019 0.002 TYR M 192 ARG 0.009 0.000 ARG 9 19 Details of bonding type rmsd hydrogen bonds : bond 0.05830 ( 1600) hydrogen bonds : angle 4.93437 ( 4428) covalent geometry : bond 0.00377 (33753) covalent geometry : angle 0.76172 (46515) Misc. bond : bond 0.10219 ( 34) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 299 time to evaluate : 6.487 Fit side-chains REVERT: C 46 LYS cc_start: 0.6567 (pmtt) cc_final: 0.6061 (tttp) REVERT: C 95 ASP cc_start: 0.7736 (t0) cc_final: 0.7308 (t70) REVERT: C 127 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8075 (mp-120) REVERT: C 256 ASN cc_start: 0.8502 (p0) cc_final: 0.8258 (p0) REVERT: M 32 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7908 (ttmt) REVERT: H 51 LYS cc_start: 0.7933 (ptmt) cc_final: 0.7149 (ptpt) REVERT: H 121 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6209 (pt0) REVERT: B 7 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6061 (pt) REVERT: B 17 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6497 (tp30) REVERT: B 22 PHE cc_start: 0.8066 (t80) cc_final: 0.7769 (t80) REVERT: D 53 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7920 (ptt-90) REVERT: E 13 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7250 (mp0) REVERT: I 20 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7625 (ttm110) REVERT: J 14 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: W 17 ASP cc_start: 0.7095 (t0) cc_final: 0.6801 (t70) REVERT: X 12 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5947 (tp30) REVERT: X 17 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6830 (mt-10) REVERT: 1 14 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7922 (pt0) REVERT: 2 33 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8020 (mp) REVERT: 6 53 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6923 (ptt-90) REVERT: 7 12 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: 0 14 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6777 (mm-30) REVERT: 0 16 LYS cc_start: 0.8256 (mttp) cc_final: 0.7982 (mttp) REVERT: e 53 ARG cc_start: 0.8547 (mtm180) cc_final: 0.8278 (mtm180) REVERT: j 12 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7813 (pp) REVERT: p 18 TRP cc_start: 0.7806 (m100) cc_final: 0.7594 (m100) outliers start: 42 outliers final: 27 residues processed: 329 average time/residue: 1.6772 time to fit residues: 654.7477 Evaluate side-chains 334 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain X residue 26 MET Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain q residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 139 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 298 optimal weight: 0.9990 chunk 264 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 297 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 295 GLN M 17 HIS H 82 ASN H 222 ASN ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 44 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.099271 restraints weight = 32110.250| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 0.86 r_work: 0.2850 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.390 33787 Z= 0.211 Angle : 0.847 14.753 46515 Z= 0.371 Chirality : 0.046 0.205 4813 Planarity : 0.005 0.059 5557 Dihedral : 19.240 176.010 6201 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.44 % Allowed : 9.02 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.14), residues: 3355 helix: 1.41 (0.12), residues: 1937 sheet: -0.01 (1.15), residues: 20 loop : 0.56 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP d 30 HIS 0.014 0.002 HIS M 17 PHE 0.025 0.002 PHE C 188 TYR 0.022 0.003 TYR j 1 ARG 0.009 0.001 ARG 9 19 Details of bonding type rmsd hydrogen bonds : bond 0.06487 ( 1600) hydrogen bonds : angle 5.11090 ( 4428) covalent geometry : bond 0.00493 (33753) covalent geometry : angle 0.84652 (46515) Misc. bond : bond 0.10467 ( 34) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 302 time to evaluate : 3.212 Fit side-chains REVERT: C 46 LYS cc_start: 0.6591 (pmtt) cc_final: 0.6094 (tttp) REVERT: C 95 ASP cc_start: 0.7762 (t0) cc_final: 0.7339 (t70) REVERT: C 127 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8191 (mp-120) REVERT: C 256 ASN cc_start: 0.8519 (p0) cc_final: 0.8286 (p0) REVERT: M 32 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7968 (ttmt) REVERT: M 215 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.8982 (t80) REVERT: H 51 LYS cc_start: 0.7982 (ptmt) cc_final: 0.7230 (ptpt) REVERT: H 121 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6340 (pt0) REVERT: B 7 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6132 (pt) REVERT: B 22 PHE cc_start: 0.8095 (t80) cc_final: 0.7802 (t80) REVERT: D 53 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7988 (ptt-90) REVERT: E 13 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7358 (mp0) REVERT: I 20 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7750 (ttm110) REVERT: J 14 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8245 (mt-10) REVERT: W 17 ASP cc_start: 0.7195 (t0) cc_final: 0.6897 (t70) REVERT: X 12 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6107 (tp30) REVERT: X 17 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6979 (mt-10) REVERT: 1 14 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8015 (pt0) REVERT: 2 33 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8045 (mp) REVERT: 6 53 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6948 (ptt-90) REVERT: 7 12 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6929 (mt-10) REVERT: 0 14 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6862 (mm-30) REVERT: 0 16 LYS cc_start: 0.8329 (mttp) cc_final: 0.8074 (mttm) REVERT: e 53 ARG cc_start: 0.8633 (mtm180) cc_final: 0.8360 (mtm180) REVERT: j 12 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7868 (pp) outliers start: 42 outliers final: 28 residues processed: 331 average time/residue: 1.6698 time to fit residues: 646.9257 Evaluate side-chains 337 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 299 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain X residue 26 MET Chi-restraints excluded: chain Y residue 5 ASP Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain q residue 16 LEU Chi-restraints excluded: chain r residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 292 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 278 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 256 optimal weight: 0.8980 chunk 251 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 295 GLN M 17 HIS H 82 ASN H 222 ASN ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.099666 restraints weight = 31970.626| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 0.93 r_work: 0.2903 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.384 33787 Z= 0.161 Angle : 0.752 13.199 46515 Z= 0.329 Chirality : 0.043 0.180 4813 Planarity : 0.005 0.046 5557 Dihedral : 18.855 179.923 6201 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.37 % Allowed : 9.26 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.60 (0.14), residues: 3355 helix: 1.68 (0.12), residues: 1900 sheet: 0.06 (1.19), residues: 20 loop : 0.36 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 5 30 HIS 0.013 0.001 HIS M 17 PHE 0.024 0.002 PHE L 146 TYR 0.019 0.002 TYR C 225 ARG 0.009 0.000 ARG 9 19 Details of bonding type rmsd hydrogen bonds : bond 0.05720 ( 1600) hydrogen bonds : angle 4.90305 ( 4428) covalent geometry : bond 0.00368 (33753) covalent geometry : angle 0.75214 (46515) Misc. bond : bond 0.10321 ( 34) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28727.94 seconds wall clock time: 495 minutes 19.77 seconds (29719.77 seconds total)