Starting phenix.real_space_refine on Tue Aug 26 01:42:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j2f_61095/08_2025/9j2f_61095.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j2f_61095/08_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_61095/08_2025/9j2f_61095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j2f_61095/08_2025/9j2f_61095.map" model { file = "/net/cci-nas-00/data/ceres_data/9j2f_61095/08_2025/9j2f_61095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j2f_61095/08_2025/9j2f_61095.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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-2': 1, 'UQ8:plan-3': 1, 'UQ8:plan-4': 1, 'UQ8:plan-5': 1, 'UQ8:plan-6': 1, 'UQ8:plan-7': 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-2': 1, 'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 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-2': 1, 'UQ8:plan-3': 1, 'UQ8:plan-6': 1, 'UQ8:plan-7': 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: 6.69, per 1000 atoms: 0.20 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: 3.08 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.81 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: 5.71 Time building geometry restraints manager: 3.86 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: 5.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 26.900 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.200 ------------------------------------------------------------------------------- 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 : 10.25 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (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 ARG 0.005 0.001 ARG q 45 TYR 0.023 0.003 TYR L 164 PHE 0.024 0.003 PHE C 188 TRP 0.027 0.003 TRP Y 30 HIS 0.012 0.002 HIS M 181 Details of bonding type rmsd covalent geometry : bond 0.01760 (33753) covalent geometry : angle 1.68909 (46515) hydrogen bonds : bond 0.15409 ( 1600) hydrogen bonds : angle 6.67921 ( 4428) 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 : 1.503 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: 0.8363 (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: 0.7310 time to fit residues: 328.6788 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 : 1.044 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 GLN C 295 GLN H 222 ASN D 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.099129 restraints weight = 32175.551| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 0.94 r_work: 0.2865 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.404 33787 Z= 0.173 Angle : 0.794 13.494 46515 Z= 0.350 Chirality : 0.044 0.184 4813 Planarity : 0.005 0.045 5557 Dihedral : 20.629 171.485 6239 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.54 % Allowed : 5.87 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.14), residues: 3355 helix: 1.59 (0.12), residues: 1901 sheet: -0.66 (0.80), residues: 32 loop : 0.18 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG 2 36 TYR 0.021 0.002 TYR C 225 PHE 0.025 0.002 PHE L 146 TRP 0.029 0.002 TRP V 30 HIS 0.009 0.001 HIS M 181 Details of bonding type rmsd covalent geometry : bond 0.00392 (33753) covalent geometry : angle 0.79385 (46515) hydrogen bonds : bond 0.06315 ( 1600) hydrogen bonds : angle 5.12917 ( 4428) Misc. bond : bond 0.10553 ( 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 366 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 321 time to evaluate : 1.173 Fit side-chains REVERT: C 46 LYS cc_start: 0.6522 (pmtt) cc_final: 0.6049 (tttp) REVERT: C 50 GLN cc_start: 0.6284 (pt0) cc_final: 0.5913 (mt0) REVERT: C 74 MET cc_start: 0.9086 (mmt) cc_final: 0.8450 (mmt) REVERT: C 95 ASP cc_start: 0.7828 (t0) cc_final: 0.7468 (t70) REVERT: C 127 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8100 (mp-120) REVERT: C 256 ASN cc_start: 0.8523 (p0) cc_final: 0.8274 (p0) REVERT: M 17 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.5809 (p90) REVERT: M 32 LYS cc_start: 0.8323 (tppp) cc_final: 0.7961 (ttmt) REVERT: M 215 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.8997 (t80) REVERT: H 51 LYS cc_start: 0.7913 (ptmt) cc_final: 0.7139 (ptpt) REVERT: H 108 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7407 (t0) REVERT: H 121 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6303 (pt0) REVERT: H 194 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6812 (tmt90) REVERT: H 225 ARG cc_start: 0.8281 (mtt90) cc_final: 0.8071 (mtt-85) REVERT: B 7 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6054 (pt) REVERT: B 22 PHE cc_start: 0.8083 (t80) cc_final: 0.7786 (t80) REVERT: E 12 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: E 13 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7269 (mp0) REVERT: J 14 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: K 2 PHE cc_start: 0.7891 (m-80) cc_final: 0.7676 (m-80) REVERT: N 17 ASP cc_start: 0.7202 (t0) cc_final: 0.6867 (t0) REVERT: R 14 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7207 (mt-10) REVERT: T 53 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8130 (mpp80) REVERT: W 17 ASP cc_start: 0.6986 (t0) cc_final: 0.6639 (t70) REVERT: W 35 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8941 (mp) REVERT: X 10 LEU cc_start: 0.7152 (mp) cc_final: 0.6796 (mp) REVERT: X 52 LYS cc_start: 0.8156 (tttp) cc_final: 0.7812 (tppt) REVERT: 6 53 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6927 (ptt-90) REVERT: 9 19 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7839 (mtm-85) REVERT: 0 14 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6842 (mm-30) REVERT: 0 16 LYS cc_start: 0.8357 (mttp) cc_final: 0.8103 (mttp) REVERT: d 34 LEU cc_start: 0.8661 (tp) cc_final: 0.8401 (tm) REVERT: e 17 ASP cc_start: 0.7588 (t0) cc_final: 0.7331 (t0) REVERT: i 12 GLU cc_start: 0.6523 (tp30) cc_final: 0.6308 (tp30) REVERT: j 12 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7844 (pp) REVERT: k 20 ARG cc_start: 0.8053 (ttt90) cc_final: 0.7794 (ttt90) REVERT: o 13 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6540 (mt-10) REVERT: r 26 MET cc_start: 0.8435 (ttp) cc_final: 0.8066 (ttt) outliers start: 45 outliers final: 26 residues processed: 356 average time/residue: 0.7245 time to fit residues: 301.9856 Evaluate side-chains 336 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 298 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 290 ASN 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 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 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 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 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 50 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 191 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 206 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 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 295 GLN H 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.098072 restraints weight = 32267.175| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 0.86 r_work: 0.2833 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.435 33787 Z= 0.227 Angle : 0.885 14.987 46515 Z= 0.388 Chirality : 0.047 0.189 4813 Planarity : 0.006 0.063 5557 Dihedral : 20.326 179.610 6226 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.78 % Allowed : 6.66 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.14), residues: 3355 helix: 1.43 (0.12), residues: 1898 sheet: -0.56 (0.82), residues: 32 loop : 0.20 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 2 36 TYR 0.022 0.003 TYR C 225 PHE 0.026 0.003 PHE C 188 TRP 0.028 0.003 TRP 2 18 HIS 0.012 0.002 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00535 (33753) covalent geometry : angle 0.88520 (46515) hydrogen bonds : bond 0.06881 ( 1600) hydrogen bonds : angle 5.24375 ( 4428) Misc. bond : bond 0.10890 ( 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 363 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 311 time to evaluate : 1.013 Fit side-chains REVERT: C 46 LYS cc_start: 0.6642 (pmtt) cc_final: 0.6203 (tttp) REVERT: C 74 MET cc_start: 0.9130 (mmt) cc_final: 0.8569 (mmt) REVERT: C 95 ASP cc_start: 0.7863 (t0) cc_final: 0.7469 (t70) REVERT: C 127 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8191 (mp-120) REVERT: C 256 ASN cc_start: 0.8535 (p0) cc_final: 0.8297 (p0) REVERT: L 139 MET cc_start: 0.9350 (mmm) cc_final: 0.9142 (mmm) REVERT: M 17 HIS cc_start: 0.6161 (OUTLIER) cc_final: 0.5924 (p90) REVERT: M 32 LYS cc_start: 0.8325 (tppp) cc_final: 0.7952 (ttmt) REVERT: M 215 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.8990 (t80) REVERT: H 51 LYS cc_start: 0.7977 (ptmt) cc_final: 0.7241 (ptpt) REVERT: H 108 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.7468 (t0) REVERT: H 121 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6422 (pt0) REVERT: H 194 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6839 (tmt90) REVERT: B 7 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6149 (pt) REVERT: B 22 PHE cc_start: 0.8102 (t80) cc_final: 0.7812 (t80) REVERT: E 12 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: E 13 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7339 (mp0) REVERT: J 14 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: R 14 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7366 (mt-10) REVERT: T 53 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8173 (mpp80) REVERT: W 17 ASP cc_start: 0.7060 (t0) cc_final: 0.6678 (t70) REVERT: W 35 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8973 (mp) REVERT: X 10 LEU cc_start: 0.7291 (mp) cc_final: 0.6974 (mp) REVERT: X 52 LYS cc_start: 0.8194 (tttp) cc_final: 0.7894 (tppt) REVERT: 9 19 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7879 (mtm-85) REVERT: 0 14 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6880 (mm-30) REVERT: 0 16 LYS cc_start: 0.8354 (mttp) cc_final: 0.8114 (mttm) REVERT: d 34 LEU cc_start: 0.8668 (tp) cc_final: 0.8333 (tm) REVERT: e 53 ARG cc_start: 0.8666 (mtm180) cc_final: 0.8409 (mtm180) REVERT: f 17 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8195 (mt-10) REVERT: h 17 ASP cc_start: 0.7470 (t0) cc_final: 0.7268 (t0) REVERT: j 12 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7910 (pp) REVERT: k 20 ARG cc_start: 0.8140 (ttt90) cc_final: 0.7847 (ttt90) REVERT: n 20 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7654 (ttm110) REVERT: o 13 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6648 (mt-10) REVERT: r 26 MET cc_start: 0.8458 (ttp) cc_final: 0.8109 (ttt) outliers start: 52 outliers final: 31 residues processed: 347 average time/residue: 0.7223 time to fit residues: 292.0435 Evaluate side-chains 343 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 300 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 108 ASN 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 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 32 THR Chi-restraints excluded: chain E residue 12 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 T residue 53 ARG Chi-restraints excluded: chain T residue 55 LEU 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 j residue 12 ILE Chi-restraints excluded: chain l residue 10 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 267 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 197 optimal weight: 8.9990 chunk 225 optimal weight: 0.0770 chunk 219 optimal weight: 0.9990 chunk 329 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7944 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.127989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.102926 restraints weight = 32370.599| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.01 r_work: 0.2926 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.318 33787 Z= 0.136 Angle : 0.699 10.760 46515 Z= 0.304 Chirality : 0.041 0.167 4813 Planarity : 0.004 0.045 5557 Dihedral : 19.204 177.143 6226 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.51 % Allowed : 7.38 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.14), residues: 3355 helix: 1.64 (0.12), residues: 1936 sheet: -0.11 (1.16), residues: 20 loop : 0.51 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 36 TYR 0.018 0.002 TYR C 225 PHE 0.022 0.002 PHE L 146 TRP 0.024 0.002 TRP d 30 HIS 0.006 0.001 HIS M 300 Details of bonding type rmsd covalent geometry : bond 0.00308 (33753) covalent geometry : angle 0.69944 (46515) hydrogen bonds : bond 0.05200 ( 1600) hydrogen bonds : angle 4.80783 ( 4428) Misc. bond : bond 0.08698 ( 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 377 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 333 time to evaluate : 0.898 Fit side-chains REVERT: C 46 LYS cc_start: 0.6411 (pmtt) cc_final: 0.5914 (tttp) REVERT: C 95 ASP cc_start: 0.7844 (t0) cc_final: 0.7459 (t70) REVERT: C 127 GLN cc_start: 0.8550 (mm-40) cc_final: 0.7999 (mp10) REVERT: C 256 ASN cc_start: 0.8496 (p0) cc_final: 0.8258 (p0) REVERT: M 32 LYS cc_start: 0.8345 (tppp) cc_final: 0.7979 (ttmt) REVERT: M 215 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8817 (t80) REVERT: H 51 LYS cc_start: 0.7924 (ptmt) cc_final: 0.7168 (ptpt) REVERT: H 108 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7313 (t0) REVERT: H 121 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6244 (pt0) REVERT: B 7 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6037 (pt) REVERT: B 22 PHE cc_start: 0.8142 (t80) cc_final: 0.7855 (t80) REVERT: E 13 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7241 (mp0) REVERT: J 14 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: W 17 ASP cc_start: 0.6984 (t0) cc_final: 0.6714 (t70) REVERT: W 35 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8918 (mp) REVERT: X 52 LYS cc_start: 0.8170 (tttp) cc_final: 0.7815 (tppt) REVERT: 6 53 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6975 (ptt-90) REVERT: 0 14 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6871 (mm-30) REVERT: 0 16 LYS cc_start: 0.8337 (mttp) cc_final: 0.8072 (mttp) REVERT: d 34 LEU cc_start: 0.8620 (tp) cc_final: 0.8195 (tm) REVERT: e 53 ARG cc_start: 0.8567 (mtm180) cc_final: 0.8298 (mtm180) REVERT: h 19 ARG cc_start: 0.8507 (mtm180) cc_final: 0.8288 (mtp180) REVERT: i 12 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5664 (mp0) REVERT: j 12 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7822 (pp) REVERT: k 20 ARG cc_start: 0.8046 (ttt90) cc_final: 0.7845 (ttt90) REVERT: n 20 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7679 (ttm110) outliers start: 44 outliers final: 21 residues processed: 363 average time/residue: 0.7046 time to fit residues: 299.8827 Evaluate side-chains 334 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 304 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 215 PHE Chi-restraints excluded: chain M residue 288 THR 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 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 6 residue 53 ARG 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 20 ARG Chi-restraints excluded: chain q residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 30 optimal weight: 0.3980 chunk 169 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 289 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 148 optimal weight: 0.0270 chunk 244 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.4240 ------------------------------------------------------------------------------- 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 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 = 0.3535 r_free = 0.3535 target = 0.132529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107832 restraints weight = 32762.074| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.01 r_work: 0.3010 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.228 33787 Z= 0.121 Angle : 0.650 13.763 46515 Z= 0.280 Chirality : 0.040 0.162 4813 Planarity : 0.004 0.044 5557 Dihedral : 18.015 179.792 6205 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.51 % Allowed : 7.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.15), residues: 3355 helix: 1.74 (0.12), residues: 1958 sheet: -0.58 (0.94), residues: 39 loop : 0.67 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 9 19 TYR 0.018 0.001 TYR C 225 PHE 0.019 0.001 PHE L 146 TRP 0.022 0.001 TRP d 30 HIS 0.005 0.001 HIS M 300 Details of bonding type rmsd covalent geometry : bond 0.00276 (33753) covalent geometry : angle 0.65015 (46515) hydrogen bonds : bond 0.04534 ( 1600) hydrogen bonds : angle 4.55090 ( 4428) Misc. bond : bond 0.06243 ( 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 390 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 346 time to evaluate : 1.158 Fit side-chains REVERT: C 46 LYS cc_start: 0.6379 (pmtt) cc_final: 0.5883 (tttp) REVERT: C 95 ASP cc_start: 0.7853 (t0) cc_final: 0.7540 (t70) REVERT: C 127 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7927 (mp10) REVERT: C 256 ASN cc_start: 0.8516 (p0) cc_final: 0.8276 (p0) REVERT: M 32 LYS cc_start: 0.8331 (tppp) cc_final: 0.7951 (ttmt) REVERT: M 215 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8897 (t80) REVERT: M 235 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7630 (mp0) REVERT: H 51 LYS cc_start: 0.7922 (ptmt) cc_final: 0.7122 (ptpt) REVERT: H 108 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.7198 (t0) REVERT: H 121 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6346 (pt0) REVERT: H 254 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: B 7 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.5934 (pt) REVERT: B 22 PHE cc_start: 0.8101 (t80) cc_final: 0.7791 (t80) REVERT: E 13 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7261 (mp0) REVERT: N 20 ARG cc_start: 0.7821 (mtp-110) cc_final: 0.7508 (mtp85) REVERT: O 7 LEU cc_start: 0.8333 (mt) cc_final: 0.8063 (mt) REVERT: T 20 ARG cc_start: 0.7163 (mtm110) cc_final: 0.6784 (mtm110) REVERT: W 17 ASP cc_start: 0.7093 (t0) cc_final: 0.6805 (t70) REVERT: W 20 ARG cc_start: 0.7943 (mtt90) cc_final: 0.7658 (mtp85) REVERT: 1 7 LEU cc_start: 0.8579 (tp) cc_final: 0.8375 (tp) REVERT: 1 14 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8023 (pt0) REVERT: 2 33 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8073 (mp) REVERT: 0 12 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.5775 (pm20) REVERT: 0 14 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6837 (mm-30) REVERT: 0 16 LYS cc_start: 0.8341 (mttp) cc_final: 0.8090 (mttp) REVERT: a 31 ILE cc_start: 0.7788 (mt) cc_final: 0.7567 (mt) REVERT: e 17 ASP cc_start: 0.7307 (t0) cc_final: 0.7001 (t0) REVERT: e 53 ARG cc_start: 0.8511 (mtm180) cc_final: 0.8211 (mtm180) REVERT: i 12 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5648 (mp0) REVERT: j 12 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7850 (pp) REVERT: n 20 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7651 (ttm110) REVERT: p 18 TRP cc_start: 0.7585 (m100) cc_final: 0.7382 (m100) REVERT: r 26 MET cc_start: 0.8366 (ttp) cc_final: 0.8089 (ttt) outliers start: 44 outliers final: 20 residues processed: 375 average time/residue: 0.7028 time to fit residues: 308.8398 Evaluate side-chains 342 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 313 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL 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 108 ASN 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 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 O residue 30 LEU Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain 2 residue 33 LEU 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 m residue 5 ASP Chi-restraints excluded: chain n residue 20 ARG Chi-restraints excluded: chain q residue 16 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 311 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 chunk 334 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 270 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 chunk 86 optimal weight: 0.0770 overall best weight: 0.9744 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103587 restraints weight = 32326.272| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.10 r_work: 0.2958 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.275 33787 Z= 0.133 Angle : 0.678 12.013 46515 Z= 0.294 Chirality : 0.040 0.168 4813 Planarity : 0.004 0.046 5557 Dihedral : 17.969 177.624 6197 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.27 % Allowed : 8.78 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.15), residues: 3355 helix: 1.79 (0.12), residues: 1952 sheet: -0.71 (1.07), residues: 29 loop : 0.76 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 9 19 TYR 0.018 0.002 TYR j 1 PHE 0.020 0.001 PHE L 146 TRP 0.024 0.002 TRP p 30 HIS 0.009 0.001 HIS M 181 Details of bonding type rmsd covalent geometry : bond 0.00299 (33753) covalent geometry : angle 0.67836 (46515) hydrogen bonds : bond 0.04985 ( 1600) hydrogen bonds : angle 4.62234 ( 4428) Misc. bond : bond 0.08111 ( 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 353 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 316 time to evaluate : 0.739 Fit side-chains REVERT: C 46 LYS cc_start: 0.6389 (pmtt) cc_final: 0.5880 (tttp) REVERT: C 95 ASP cc_start: 0.7784 (t0) cc_final: 0.7460 (t70) REVERT: C 127 GLN cc_start: 0.8487 (mm-40) cc_final: 0.7982 (mp-120) REVERT: C 256 ASN cc_start: 0.8512 (p0) cc_final: 0.8284 (p0) REVERT: M 32 LYS cc_start: 0.8329 (tppp) cc_final: 0.7942 (ttmt) REVERT: H 51 LYS cc_start: 0.7908 (ptmt) cc_final: 0.7100 (ptpt) REVERT: H 108 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.7257 (t0) REVERT: H 121 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6266 (pt0) REVERT: B 7 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.5949 (pt) REVERT: B 22 PHE cc_start: 0.8063 (t80) cc_final: 0.7783 (t80) REVERT: E 13 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7173 (mp0) REVERT: J 14 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: T 20 ARG cc_start: 0.7133 (mtm110) cc_final: 0.6746 (mtm110) REVERT: W 17 ASP cc_start: 0.7095 (t0) cc_final: 0.6761 (t70) REVERT: W 20 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7612 (mtp85) REVERT: X 12 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5956 (tp30) REVERT: 2 33 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8064 (mp) REVERT: 9 17 ASP cc_start: 0.7328 (t0) cc_final: 0.7126 (t0) REVERT: 0 12 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.5696 (pm20) REVERT: 0 14 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6786 (mm-30) REVERT: 0 16 LYS cc_start: 0.8309 (mttp) cc_final: 0.8029 (mttp) REVERT: b 20 ARG cc_start: 0.7858 (ttt-90) cc_final: 0.6986 (ttt90) REVERT: e 53 ARG cc_start: 0.8509 (mtm180) cc_final: 0.8215 (mtm180) REVERT: j 12 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7847 (pp) REVERT: n 20 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7603 (ttm110) REVERT: p 18 TRP cc_start: 0.7553 (m100) cc_final: 0.7341 (m100) outliers start: 37 outliers final: 19 residues processed: 339 average time/residue: 0.7035 time to fit residues: 279.8798 Evaluate side-chains 330 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 303 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL 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 108 ASN 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 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 12 GLU Chi-restraints excluded: chain 2 residue 33 LEU 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 n residue 20 ARG Chi-restraints excluded: chain q residue 16 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 218 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 173 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 254 optimal weight: 0.7980 chunk 246 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 H 82 ASN H 222 ASN ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.101111 restraints weight = 32154.687| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.00 r_work: 0.2894 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.309 33787 Z= 0.149 Angle : 0.722 13.679 46515 Z= 0.313 Chirality : 0.042 0.175 4813 Planarity : 0.004 0.045 5557 Dihedral : 18.190 176.722 6197 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.30 % Allowed : 8.75 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.15), residues: 3355 helix: 1.72 (0.12), residues: 1950 sheet: 0.13 (1.15), residues: 20 loop : 0.72 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 9 19 TYR 0.018 0.002 TYR M 192 PHE 0.021 0.002 PHE L 146 TRP 0.026 0.002 TRP p 30 HIS 0.009 0.001 HIS M 181 Details of bonding type rmsd covalent geometry : bond 0.00337 (33753) covalent geometry : angle 0.72239 (46515) hydrogen bonds : bond 0.05449 ( 1600) hydrogen bonds : angle 4.76928 ( 4428) Misc. bond : bond 0.09239 ( 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 357 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 319 time to evaluate : 1.024 Fit side-chains REVERT: C 46 LYS cc_start: 0.6490 (pmtt) cc_final: 0.5986 (tttp) REVERT: C 95 ASP cc_start: 0.7822 (t0) cc_final: 0.7506 (t70) REVERT: C 127 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8046 (mp-120) REVERT: C 256 ASN cc_start: 0.8544 (p0) cc_final: 0.8314 (p0) REVERT: M 32 LYS cc_start: 0.8344 (tppp) cc_final: 0.7967 (ttmt) REVERT: H 51 LYS cc_start: 0.7947 (ptmt) cc_final: 0.7160 (ptpt) REVERT: H 108 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7310 (t0) REVERT: H 121 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6321 (pt0) REVERT: B 7 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.5973 (pt) REVERT: B 22 PHE cc_start: 0.8065 (t80) cc_final: 0.7754 (t80) REVERT: E 13 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7250 (mp0) REVERT: J 14 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: T 20 ARG cc_start: 0.7128 (mtm110) cc_final: 0.6742 (mtm110) REVERT: W 17 ASP cc_start: 0.7027 (t0) cc_final: 0.6687 (t70) REVERT: W 20 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7639 (mtp85) REVERT: X 12 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6056 (tp30) REVERT: 1 14 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7971 (pt0) REVERT: 2 33 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8078 (mp) REVERT: 7 12 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: 0 12 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6297 (tt0) REVERT: 0 14 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6840 (mm-30) REVERT: 0 16 LYS cc_start: 0.8304 (mttp) cc_final: 0.8094 (mttp) REVERT: e 17 ASP cc_start: 0.7230 (t0) cc_final: 0.6929 (t0) REVERT: e 53 ARG cc_start: 0.8573 (mtm180) cc_final: 0.8272 (mtm180) REVERT: j 12 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7819 (pp) REVERT: n 20 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7646 (ttm110) outliers start: 38 outliers final: 20 residues processed: 344 average time/residue: 0.7037 time to fit residues: 282.6795 Evaluate side-chains 330 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 301 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL 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 H residue 108 ASN 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 R residue 55 VAL Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain Y residue 5 ASP Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain a 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 20 ARG 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 252 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 168 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 165 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 290 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.099710 restraints weight = 32047.818| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 0.86 r_work: 0.2859 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.338 33787 Z= 0.186 Angle : 0.803 13.633 46515 Z= 0.350 Chirality : 0.044 0.187 4813 Planarity : 0.005 0.051 5557 Dihedral : 18.780 173.085 6195 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.06 % Allowed : 9.19 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.14), residues: 3355 helix: 1.57 (0.12), residues: 1934 sheet: 0.12 (1.14), residues: 20 loop : 0.65 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 9 19 TYR 0.020 0.002 TYR M 192 PHE 0.022 0.002 PHE L 146 TRP 0.029 0.002 TRP G 30 HIS 0.011 0.002 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00429 (33753) covalent geometry : angle 0.80254 (46515) hydrogen bonds : bond 0.06155 ( 1600) hydrogen bonds : angle 4.99614 ( 4428) Misc. bond : bond 0.09998 ( 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 343 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 312 time to evaluate : 3.120 Fit side-chains REVERT: C 46 LYS cc_start: 0.6534 (pmtt) cc_final: 0.6075 (tttp) REVERT: C 95 ASP cc_start: 0.7825 (t0) cc_final: 0.7493 (t70) REVERT: C 127 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8149 (mp-120) REVERT: C 256 ASN cc_start: 0.8558 (p0) cc_final: 0.8333 (p0) REVERT: M 32 LYS cc_start: 0.8299 (tppp) cc_final: 0.7914 (ttmt) REVERT: M 215 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.9070 (t80) REVERT: H 51 LYS cc_start: 0.7959 (ptmt) cc_final: 0.7192 (ptpt) REVERT: H 108 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7402 (t0) REVERT: H 121 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6324 (pt0) REVERT: B 7 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6101 (pt) REVERT: B 22 PHE cc_start: 0.8116 (t80) cc_final: 0.7804 (t80) REVERT: E 13 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7324 (mp0) REVERT: J 14 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: T 20 ARG cc_start: 0.7159 (mtm110) cc_final: 0.6757 (mtm110) REVERT: W 17 ASP cc_start: 0.7099 (t0) cc_final: 0.6755 (t70) REVERT: W 20 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7690 (mtp85) REVERT: X 12 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6000 (tp30) REVERT: 2 33 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8037 (mp) REVERT: 7 12 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6869 (mt-10) REVERT: 0 12 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6335 (tt0) REVERT: 0 14 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6805 (mm-30) REVERT: e 53 ARG cc_start: 0.8619 (mtm180) cc_final: 0.8360 (mtm180) REVERT: j 12 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7829 (pp) REVERT: n 20 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7644 (ttm110) outliers start: 31 outliers final: 18 residues processed: 335 average time/residue: 0.7344 time to fit residues: 286.8922 Evaluate side-chains 329 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 301 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL 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 H residue 108 ASN 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 X residue 12 GLU Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain a 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 20 ARG 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 168 optimal weight: 0.0970 chunk 223 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 283 optimal weight: 0.7980 chunk 172 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 H 72 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 = 0.3436 r_free = 0.3436 target = 0.125024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.099478 restraints weight = 32069.921| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 0.99 r_work: 0.2848 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.346 33787 Z= 0.176 Angle : 0.778 13.435 46515 Z= 0.339 Chirality : 0.044 0.184 4813 Planarity : 0.005 0.045 5557 Dihedral : 18.771 174.616 6195 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.17 % Allowed : 9.37 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.14), residues: 3355 helix: 1.56 (0.12), residues: 1934 sheet: 0.06 (1.13), residues: 20 loop : 0.64 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 9 19 TYR 0.020 0.002 TYR M 192 PHE 0.023 0.002 PHE L 146 TRP 0.026 0.002 TRP G 30 HIS 0.010 0.001 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00405 (33753) covalent geometry : angle 0.77812 (46515) hydrogen bonds : bond 0.05940 ( 1600) hydrogen bonds : angle 4.94695 ( 4428) Misc. bond : bond 0.09991 ( 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 333 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 0.865 Fit side-chains REVERT: C 46 LYS cc_start: 0.6523 (pmtt) cc_final: 0.6031 (tttp) REVERT: C 95 ASP cc_start: 0.7808 (t0) cc_final: 0.7477 (t70) REVERT: C 127 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8150 (mp-120) REVERT: C 256 ASN cc_start: 0.8572 (p0) cc_final: 0.8348 (p0) REVERT: M 32 LYS cc_start: 0.8323 (tppp) cc_final: 0.7950 (ttmt) REVERT: H 51 LYS cc_start: 0.7947 (ptmt) cc_final: 0.7163 (ptpt) REVERT: H 108 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7367 (t0) REVERT: H 121 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6307 (pt0) REVERT: B 7 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6025 (pt) REVERT: B 22 PHE cc_start: 0.8097 (t80) cc_final: 0.7793 (t80) REVERT: E 13 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7328 (mp0) REVERT: J 14 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: T 20 ARG cc_start: 0.7149 (mtm110) cc_final: 0.6744 (mtm110) REVERT: W 17 ASP cc_start: 0.7101 (t0) cc_final: 0.6766 (t70) REVERT: W 20 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7553 (mtp85) REVERT: X 12 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6045 (tp30) REVERT: 1 14 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7961 (pt0) REVERT: 2 33 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8002 (mp) REVERT: 7 12 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6898 (mt-10) REVERT: 0 12 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6386 (tt0) REVERT: 0 14 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6825 (mm-30) REVERT: e 53 ARG cc_start: 0.8626 (mtm180) cc_final: 0.8370 (mtm180) REVERT: j 12 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7850 (pp) outliers start: 34 outliers final: 19 residues processed: 326 average time/residue: 0.7722 time to fit residues: 292.1574 Evaluate side-chains 326 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 299 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL 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 288 THR Chi-restraints excluded: chain H residue 108 ASN 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 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 2 residue 33 LEU Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain a residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain j residue 12 ILE 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 197 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 195 optimal weight: 7.9990 chunk 333 optimal weight: 7.9990 chunk 165 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 overall best weight: 4.5986 ------------------------------------------------------------------------------- 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 H 72 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 = 0.3400 r_free = 0.3400 target = 0.122343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.098846 restraints weight = 32287.283| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 0.83 r_work: 0.2836 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.381 33787 Z= 0.254 Angle : 0.923 14.979 46515 Z= 0.402 Chirality : 0.049 0.222 4813 Planarity : 0.006 0.075 5557 Dihedral : 19.466 179.396 6195 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.17 % Allowed : 9.40 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.14), residues: 3355 helix: 1.41 (0.12), residues: 1899 sheet: -0.04 (1.11), residues: 20 loop : 0.37 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 9 19 TYR 0.024 0.003 TYR L 51 PHE 0.028 0.003 PHE L 34 TRP 0.032 0.003 TRP G 30 HIS 0.017 0.002 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00601 (33753) covalent geometry : angle 0.92289 (46515) hydrogen bonds : bond 0.06953 ( 1600) hydrogen bonds : angle 5.23329 ( 4428) Misc. bond : bond 0.10541 ( 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 342 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 308 time to evaluate : 1.162 Fit side-chains REVERT: C 95 ASP cc_start: 0.7811 (t0) cc_final: 0.7482 (t70) REVERT: C 127 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8157 (mp-120) REVERT: C 256 ASN cc_start: 0.8516 (p0) cc_final: 0.8275 (p0) REVERT: M 17 HIS cc_start: 0.6132 (p-80) cc_final: 0.5879 (p90) REVERT: M 32 LYS cc_start: 0.8288 (tppp) cc_final: 0.7964 (ttmt) REVERT: H 51 LYS cc_start: 0.7955 (ptmt) cc_final: 0.7205 (ptpt) REVERT: H 58 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7283 (mm-40) REVERT: H 108 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7452 (t0) REVERT: H 121 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6300 (pt0) REVERT: B 7 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6203 (pt) REVERT: B 22 PHE cc_start: 0.8094 (t80) cc_final: 0.7809 (t80) REVERT: E 13 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7323 (mp0) REVERT: J 14 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: W 17 ASP cc_start: 0.6932 (t0) cc_final: 0.6516 (t70) REVERT: W 20 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7577 (mtp85) REVERT: 2 33 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8032 (mp) REVERT: 7 12 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6900 (mt-10) REVERT: 0 14 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6820 (mm-30) REVERT: e 17 ASP cc_start: 0.7648 (t0) cc_final: 0.7385 (t0) REVERT: e 53 ARG cc_start: 0.8620 (mtm180) cc_final: 0.8409 (mtm180) REVERT: i 12 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5872 (mp0) REVERT: j 12 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7877 (pp) outliers start: 34 outliers final: 23 residues processed: 332 average time/residue: 0.7527 time to fit residues: 290.3779 Evaluate side-chains 327 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL 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 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 108 ASN 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 B residue 32 THR 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 9 VAL Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain a residue 8 VAL 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 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 7 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 140 optimal weight: 0.0670 chunk 254 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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 H 72 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 = 0.3439 r_free = 0.3439 target = 0.125268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.098998 restraints weight = 32217.625| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 0.95 r_work: 0.2895 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.358 33787 Z= 0.162 Angle : 0.759 13.224 46515 Z= 0.330 Chirality : 0.043 0.184 4813 Planarity : 0.005 0.045 5557 Dihedral : 18.943 179.711 6195 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.99 % Allowed : 9.61 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.14), residues: 3355 helix: 1.55 (0.12), residues: 1934 sheet: -0.04 (1.13), residues: 20 loop : 0.60 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 9 19 TYR 0.018 0.002 TYR C 225 PHE 0.024 0.002 PHE L 146 TRP 0.026 0.002 TRP 5 30 HIS 0.009 0.001 HIS M 181 Details of bonding type rmsd covalent geometry : bond 0.00371 (33753) covalent geometry : angle 0.75866 (46515) hydrogen bonds : bond 0.05742 ( 1600) hydrogen bonds : angle 4.91940 ( 4428) Misc. bond : bond 0.10163 ( 34) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12694.04 seconds wall clock time: 216 minutes 19.91 seconds (12979.91 seconds total)