Starting phenix.real_space_refine on Mon Jul 6 03:26:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j2f_61095/07_2026/9j2f_61095.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j2f_61095/07_2026/9j2f_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j2f_61095/07_2026/9j2f_61095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j2f_61095/07_2026/9j2f_61095.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j2f_61095/07_2026/9j2f_61095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j2f_61095/07_2026/9j2f_61095.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 518 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'BCB': 2, 'BPB': 1, 'CDL': 1, 'LMT': 1, 'MQ7': 1, 'NS5': 1, 'PGV': 1, 'UQ8': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain breaks: 1 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: 7.23, per 1000 atoms: 0.22 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: 3.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 11 sheets defined 63.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 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: 4.46 Time building geometry restraints manager: 3.77 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=" 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 bond pdb=" CAB HEC C 401 " pdb=" CBB HEC C 401 " ideal model delta sigma weight residual 1.544 1.328 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" CAB HEC C 404 " pdb=" CBB HEC C 404 " ideal model delta sigma weight residual 1.544 1.330 0.214 2.00e-02 2.50e+03 1.15e+02 ... (remaining 33748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 43550 3.14 - 6.28: 2181 6.28 - 9.43: 519 9.43 - 12.57: 208 12.57 - 15.71: 57 Bond angle restraints: 46515 Sorted by residual: angle pdb=" C1C BCB M 402 " pdb=" C2C BCB M 402 " pdb=" C3C BCB M 402 " ideal model delta sigma weight residual 102.19 90.62 11.57 1.73e+00 3.36e-01 4.49e+01 angle pdb=" C1C BCB L 303 " pdb=" C2C BCB L 303 " pdb=" C3C BCB L 303 " ideal model delta sigma weight residual 102.19 90.71 11.47 1.73e+00 3.36e-01 4.42e+01 angle pdb=" C1C BCB k 102 " pdb=" C2C BCB k 102 " pdb=" C3C BCB k 102 " ideal model delta sigma weight residual 102.19 90.78 11.41 1.73e+00 3.36e-01 4.37e+01 angle pdb=" C1C BCB N 101 " pdb=" C2C BCB N 101 " pdb=" C3C BCB N 101 " ideal model delta sigma weight residual 102.19 91.07 11.12 1.73e+00 3.36e-01 4.15e+01 angle pdb=" C1C BCB h 102 " pdb=" C2C BCB h 102 " pdb=" C3C BCB h 102 " ideal model delta sigma weight residual 102.19 91.08 11.10 1.73e+00 3.36e-01 4.14e+01 ... (remaining 46510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 17969 35.05 - 70.09: 670 70.09 - 105.14: 97 105.14 - 140.19: 31 140.19 - 175.24: 14 Dihedral angle restraints: 18781 sinusoidal: 8786 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 18778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4051 0.074 - 0.148: 614 0.148 - 0.223: 87 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 3.000 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: 5.370 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.750 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 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= 0.853 Angle : 1.695 15.709 46515 Z= 0.741 Chirality : 0.060 0.371 4813 Planarity : 0.015 0.233 5557 Dihedral : 18.877 175.237 12325 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 are 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/Z covalent geometry : bond 0.01759 / 0.76 (33753) covalent geometry : angle 1.69478 / 0.74 (46515) hydrogen bonds : bond 0.15409 / 10.64 ( 1600) hydrogen bonds : angle 6.67921 / 4.89 ( 4428) Misc. bond : bond 0.13368 / 8.95 ( 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 : 1.144 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: 0.8062 (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: 0.7613 time to fit residues: 345.0930 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 : 1.108 ------------------------------------------------------------------------------- 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... 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 = 0.3436 r_free = 0.3436 target = 0.125065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.098902 restraints weight = 32225.407| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 0.95 r_work: 0.2890 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.397 33787 Z= 0.172 Angle : 0.796 12.638 46515 Z= 0.347 Chirality : 0.043 0.183 4813 Planarity : 0.005 0.044 5557 Dihedral : 20.092 173.063 6319 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.48 % Allowed : 5.93 % 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 are not related in a simple way. whole: 1.43 (0.14), residues: 3355 helix: 1.61 (0.12), residues: 1901 sheet: -0.64 (0.80), residues: 32 loop : 0.19 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG 2 36 TYR 0.021 0.002 TYR C 225 PHE 0.025 0.002 PHE L 146 TRP 0.030 0.002 TRP V 30 HIS 0.009 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (33753) covalent geometry : angle 0.79629 / 0.35 (46515) hydrogen bonds : bond 0.06136 / 4.21 ( 1600) hydrogen bonds : angle 5.09948 / 3.72 ( 4428) Misc. bond : bond 0.10238 / 6.18 ( 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 363 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 320 time to evaluate : 1.149 Fit side-chains REVERT: C 46 LYS cc_start: 0.6462 (pmtt) cc_final: 0.6006 (tttp) REVERT: C 50 GLN cc_start: 0.6256 (pt0) cc_final: 0.5910 (mt0) REVERT: C 74 MET cc_start: 0.9066 (mmt) cc_final: 0.8410 (mmt) REVERT: C 95 ASP cc_start: 0.7827 (t0) cc_final: 0.7453 (t70) REVERT: C 127 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8077 (mp-120) REVERT: C 256 ASN cc_start: 0.8492 (p0) cc_final: 0.8239 (p0) REVERT: L 72 LYS cc_start: 0.8869 (pttp) cc_final: 0.8627 (pttm) REVERT: M 17 HIS cc_start: 0.6132 (p-80) cc_final: 0.5861 (p90) REVERT: M 32 LYS cc_start: 0.8303 (tppp) cc_final: 0.7945 (ttmt) REVERT: M 215 PHE cc_start: 0.9394 (OUTLIER) cc_final: 0.8947 (t80) REVERT: H 51 LYS cc_start: 0.7903 (ptmt) cc_final: 0.7130 (ptpt) REVERT: H 108 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7407 (t0) REVERT: H 121 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6249 (pt0) REVERT: H 194 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.6798 (tmt90) REVERT: H 225 ARG cc_start: 0.8271 (mtt90) cc_final: 0.8064 (mtt-85) REVERT: B 7 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6050 (pt) REVERT: B 22 PHE cc_start: 0.8068 (t80) cc_final: 0.7774 (t80) REVERT: E 12 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: E 13 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7224 (mp0) REVERT: J 14 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: K 2 PHE cc_start: 0.7861 (m-80) cc_final: 0.7656 (m-80) REVERT: N 17 ASP cc_start: 0.7134 (t0) cc_final: 0.6821 (t0) REVERT: R 14 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7174 (mt-10) REVERT: T 53 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8123 (mpp80) REVERT: W 17 ASP cc_start: 0.6941 (t0) cc_final: 0.6593 (t70) REVERT: W 35 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8931 (mp) REVERT: X 52 LYS cc_start: 0.8135 (tttp) cc_final: 0.7804 (tppt) REVERT: 1 14 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8130 (mt-10) REVERT: 6 53 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6974 (ptt-90) REVERT: 9 19 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7801 (mtm-85) REVERT: 0 14 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6812 (mm-30) REVERT: 0 16 LYS cc_start: 0.8324 (mttp) cc_final: 0.8082 (mttm) REVERT: d 34 LEU cc_start: 0.8675 (tp) cc_final: 0.8409 (tm) REVERT: e 17 ASP cc_start: 0.7540 (t0) cc_final: 0.7304 (t0) REVERT: e 53 ARG cc_start: 0.8517 (mtm180) cc_final: 0.8281 (mtm180) REVERT: i 12 GLU cc_start: 0.6449 (tp30) cc_final: 0.6226 (tp30) REVERT: j 12 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7837 (pp) REVERT: k 20 ARG cc_start: 0.8034 (ttt90) cc_final: 0.7788 (ttt90) REVERT: o 13 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6513 (mt-10) REVERT: r 26 MET cc_start: 0.8413 (ttp) cc_final: 0.8041 (ttt) outliers start: 43 outliers final: 24 residues processed: 355 average time/residue: 0.7148 time to fit residues: 297.3339 Evaluate side-chains 333 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 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 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: 4.9990 chunk 206 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 ASN C 295 GLN H 82 ASN H 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.099752 restraints weight = 32283.712| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 0.83 r_work: 0.2863 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.396 33787 Z= 0.186 Angle : 0.812 14.493 46515 Z= 0.355 Chirality : 0.044 0.181 4813 Planarity : 0.005 0.046 5557 Dihedral : 19.577 177.980 6304 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.68 % Allowed : 6.55 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.14), residues: 3355 helix: 1.45 (0.12), residues: 1937 sheet: -0.53 (0.83), residues: 32 loop : 0.45 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 2 36 TYR 0.020 0.002 TYR C 225 PHE 0.025 0.002 PHE L 146 TRP 0.025 0.002 TRP d 30 HIS 0.009 0.002 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (33753) covalent geometry : angle 0.81220 / 0.36 (46515) hydrogen bonds : bond 0.06318 / 4.34 ( 1600) hydrogen bonds : angle 5.08924 / 3.71 ( 4428) Misc. bond : bond 0.10403 / 6.22 ( 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 365 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 1.163 Fit side-chains REVERT: C 46 LYS cc_start: 0.6483 (pmtt) cc_final: 0.6011 (ttmt) REVERT: C 74 MET cc_start: 0.9099 (mmt) cc_final: 0.8507 (mmt) REVERT: C 95 ASP cc_start: 0.7848 (t0) cc_final: 0.7449 (t70) REVERT: C 127 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8168 (mp-120) REVERT: C 256 ASN cc_start: 0.8540 (p0) cc_final: 0.8314 (p0) REVERT: L 72 LYS cc_start: 0.8906 (pttp) cc_final: 0.8687 (pttm) REVERT: M 17 HIS cc_start: 0.6147 (p-80) cc_final: 0.5921 (p90) REVERT: M 32 LYS cc_start: 0.8311 (tppp) cc_final: 0.7937 (ttmt) REVERT: M 215 PHE cc_start: 0.9394 (OUTLIER) cc_final: 0.8944 (t80) REVERT: H 51 LYS cc_start: 0.7963 (ptmt) cc_final: 0.7222 (ptpt) REVERT: H 108 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.7413 (t0) REVERT: H 121 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6401 (pt0) REVERT: H 194 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.6855 (tmt90) REVERT: B 7 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6079 (pt) REVERT: B 22 PHE cc_start: 0.8092 (t80) cc_final: 0.7802 (t80) REVERT: E 12 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: E 13 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7325 (mp0) REVERT: J 14 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: K 2 PHE cc_start: 0.7877 (m-80) cc_final: 0.7651 (m-80) REVERT: R 14 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7277 (mt-10) REVERT: T 53 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8148 (mpp80) REVERT: W 17 ASP cc_start: 0.7002 (t0) cc_final: 0.6616 (t70) REVERT: W 35 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8917 (mp) REVERT: X 52 LYS cc_start: 0.8193 (tttp) cc_final: 0.7867 (tppt) REVERT: 1 14 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8168 (mt-10) REVERT: 6 53 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6971 (ptt-90) REVERT: 9 19 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7866 (mtm-85) REVERT: 0 14 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6853 (mm-30) REVERT: 0 16 LYS cc_start: 0.8320 (mttp) cc_final: 0.8079 (mttm) REVERT: d 34 LEU cc_start: 0.8670 (tp) cc_final: 0.8308 (tm) REVERT: i 12 GLU cc_start: 0.6562 (tp30) cc_final: 0.5824 (mp0) REVERT: j 12 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7843 (pp) REVERT: k 20 ARG cc_start: 0.8116 (ttt90) cc_final: 0.7841 (ttt90) REVERT: n 20 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7630 (ttm110) REVERT: o 13 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6598 (mt-10) REVERT: r 26 MET cc_start: 0.8430 (ttp) cc_final: 0.8068 (ttt) outliers start: 49 outliers final: 28 residues processed: 350 average time/residue: 0.7228 time to fit residues: 297.2857 Evaluate side-chains 339 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 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 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 R residue 55 VAL 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 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: 4.9990 chunk 91 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 219 optimal weight: 0.0170 chunk 329 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 295 GLN H 82 ASN H 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.098443 restraints weight = 32186.324| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 0.93 r_work: 0.2847 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.399 33787 Z= 0.194 Angle : 0.825 14.488 46515 Z= 0.361 Chirality : 0.045 0.185 4813 Planarity : 0.005 0.050 5557 Dihedral : 19.469 178.750 6303 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.75 % Allowed : 7.07 % Favored : 91.18 % 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 are not related in a simple way. whole: 1.43 (0.14), residues: 3355 helix: 1.43 (0.12), residues: 1937 sheet: -0.49 (0.83), residues: 32 loop : 0.45 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 2 36 TYR 0.021 0.002 TYR C 225 PHE 0.025 0.002 PHE L 146 TRP 0.026 0.002 TRP G 30 HIS 0.010 0.002 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (33753) covalent geometry : angle 0.82514 / 0.36 (46515) hydrogen bonds : bond 0.06349 / 4.37 ( 1600) hydrogen bonds : angle 5.09030 / 3.70 ( 4428) Misc. bond : bond 0.10439 / 6.28 ( 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 362 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 311 time to evaluate : 1.201 Fit side-chains REVERT: C 46 LYS cc_start: 0.6531 (pmtt) cc_final: 0.6081 (tttp) REVERT: C 50 GLN cc_start: 0.6272 (pt0) cc_final: 0.6057 (mt0) REVERT: C 74 MET cc_start: 0.9099 (mmt) cc_final: 0.8559 (mmt) REVERT: C 95 ASP cc_start: 0.7842 (t0) cc_final: 0.7448 (t70) REVERT: C 127 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8185 (mp-120) REVERT: C 256 ASN cc_start: 0.8548 (p0) cc_final: 0.8328 (p0) REVERT: L 72 LYS cc_start: 0.8903 (pttp) cc_final: 0.8664 (pttm) REVERT: M 17 HIS cc_start: 0.6178 (p-80) cc_final: 0.5951 (p90) REVERT: M 32 LYS cc_start: 0.8323 (tppp) cc_final: 0.7945 (ttmt) REVERT: M 215 PHE cc_start: 0.9399 (OUTLIER) cc_final: 0.8970 (t80) REVERT: H 51 LYS cc_start: 0.7963 (ptmt) cc_final: 0.7208 (ptpt) REVERT: H 108 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7401 (t0) REVERT: H 121 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6387 (pt0) REVERT: H 194 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6812 (tmt90) REVERT: B 7 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6061 (pt) REVERT: B 22 PHE cc_start: 0.8109 (t80) cc_final: 0.7809 (t80) REVERT: E 13 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7302 (mp0) REVERT: J 14 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8253 (mt-10) REVERT: T 53 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8120 (mpp80) REVERT: W 17 ASP cc_start: 0.7007 (t0) cc_final: 0.6621 (t70) REVERT: W 35 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8933 (mp) REVERT: X 12 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6129 (tp30) REVERT: X 17 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6980 (tt0) REVERT: X 52 LYS cc_start: 0.8183 (tttp) cc_final: 0.7861 (tppt) REVERT: 6 53 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6974 (ptt-90) REVERT: 9 19 ARG cc_start: 0.8129 (mtm-85) cc_final: 0.7881 (mtm-85) REVERT: 0 14 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6864 (mm-30) REVERT: 0 16 LYS cc_start: 0.8350 (mttp) cc_final: 0.8105 (mttm) REVERT: d 34 LEU cc_start: 0.8650 (tp) cc_final: 0.8230 (tm) REVERT: e 53 ARG cc_start: 0.8611 (mtm180) cc_final: 0.8401 (mtm180) REVERT: i 12 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5830 (mp0) REVERT: j 12 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7866 (pp) REVERT: k 20 ARG cc_start: 0.8091 (ttt90) cc_final: 0.7829 (ttt90) REVERT: o 13 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6567 (mt-10) REVERT: r 26 MET cc_start: 0.8433 (ttp) cc_final: 0.8076 (ttt) outliers start: 51 outliers final: 30 residues processed: 348 average time/residue: 0.7533 time to fit residues: 308.1094 Evaluate side-chains 340 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 298 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 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 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 P residue 9 VAL 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 W residue 35 LEU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain i residue 12 GLU Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain l residue 10 LEU Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain q residue 16 LEU Chi-restraints excluded: chain r residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 30 optimal weight: 0.5980 chunk 169 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 289 optimal weight: 9.9990 chunk 249 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 295 GLN H 82 ASN H 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.098127 restraints weight = 32303.450| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 0.95 r_work: 0.2887 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.361 33787 Z= 0.168 Angle : 0.770 13.917 46515 Z= 0.337 Chirality : 0.043 0.178 4813 Planarity : 0.005 0.045 5557 Dihedral : 19.138 177.124 6298 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.58 % Allowed : 7.65 % Favored : 90.77 % 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 are not related in a simple way. whole: 1.54 (0.14), residues: 3355 helix: 1.51 (0.12), residues: 1937 sheet: -0.07 (1.16), residues: 20 loop : 0.50 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 10 TYR 0.020 0.002 TYR C 225 PHE 0.024 0.002 PHE L 146 TRP 0.026 0.002 TRP d 30 HIS 0.009 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (33753) covalent geometry : angle 0.77047 / 0.34 (46515) hydrogen bonds : bond 0.05905 / 4.06 ( 1600) hydrogen bonds : angle 4.96999 / 3.62 ( 4428) Misc. bond : bond 0.09924 / 6.08 ( 34) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6710 Ramachandran restraints generated. 3355 Oldfield, 0 Emsley, 3355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 315 time to evaluate : 1.058 Fit side-chains REVERT: C 46 LYS cc_start: 0.6457 (pmtt) cc_final: 0.5982 (tttp) REVERT: C 74 MET cc_start: 0.9039 (mmt) cc_final: 0.8441 (mmt) REVERT: C 95 ASP cc_start: 0.7827 (t0) cc_final: 0.7417 (t70) REVERT: C 127 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8102 (mp-120) REVERT: C 256 ASN cc_start: 0.8513 (p0) cc_final: 0.8270 (p0) REVERT: M 32 LYS cc_start: 0.8297 (tppp) cc_final: 0.7924 (ttmt) REVERT: M 215 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8948 (t80) REVERT: H 51 LYS cc_start: 0.7942 (ptmt) cc_final: 0.7165 (ptpt) REVERT: H 108 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7375 (t0) REVERT: H 121 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6237 (pt0) REVERT: H 194 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6797 (tmt90) REVERT: B 7 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6012 (pt) REVERT: B 22 PHE cc_start: 0.8076 (t80) cc_final: 0.7774 (t80) REVERT: E 13 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7194 (mp0) REVERT: J 14 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: T 53 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8085 (mpp80) REVERT: W 17 ASP cc_start: 0.7021 (t0) cc_final: 0.6725 (t70) REVERT: W 35 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8902 (mp) REVERT: X 12 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6020 (tp30) REVERT: X 17 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6863 (tt0) REVERT: X 52 LYS cc_start: 0.8154 (tttp) cc_final: 0.7833 (tppt) REVERT: 2 33 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7985 (mp) REVERT: 6 53 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6969 (ptt-90) REVERT: 7 12 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6835 (mt-10) REVERT: 0 14 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6794 (mm-30) REVERT: 0 16 LYS cc_start: 0.8270 (mttp) cc_final: 0.7992 (mttp) REVERT: e 53 ARG cc_start: 0.8535 (mtm180) cc_final: 0.8317 (mtm180) REVERT: f 17 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8101 (mt-10) REVERT: h 17 ASP cc_start: 0.7221 (t0) cc_final: 0.6997 (t0) REVERT: i 12 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5758 (mp0) REVERT: j 12 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7825 (pp) REVERT: o 13 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6492 (mt-10) REVERT: r 26 MET cc_start: 0.8391 (ttp) cc_final: 0.8029 (ttt) outliers start: 46 outliers final: 27 residues processed: 349 average time/residue: 0.7010 time to fit residues: 286.9129 Evaluate side-chains 342 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 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 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 T residue 53 ARG Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain i residue 12 GLU Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 311 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 265 optimal weight: 0.0370 chunk 334 optimal weight: 0.0370 chunk 120 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 270 optimal weight: 0.7980 chunk 201 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 50 GLN C 295 GLN H 82 ASN H 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.106077 restraints weight = 32462.879| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 0.93 r_work: 0.2982 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.267 33787 Z= 0.126 Angle : 0.666 11.979 46515 Z= 0.288 Chirality : 0.040 0.160 4813 Planarity : 0.004 0.045 5557 Dihedral : 18.221 179.424 6298 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.65 % Allowed : 7.86 % 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 are not related in a simple way. whole: 1.78 (0.15), residues: 3355 helix: 1.70 (0.12), residues: 1958 sheet: 0.00 (1.01), residues: 30 loop : 0.61 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 9 19 TYR 0.018 0.001 TYR W 28 PHE 0.023 0.001 PHE B 18 TRP 0.023 0.001 TRP d 30 HIS 0.006 0.001 HIS M 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (33753) covalent geometry : angle 0.66635 / 0.29 (46515) hydrogen bonds : bond 0.04764 / 3.26 ( 1600) hydrogen bonds : angle 4.64487 / 3.38 ( 4428) Misc. bond : bond 0.07605 / 4.69 ( 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 387 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 339 time to evaluate : 1.081 Fit side-chains REVERT: C 46 LYS cc_start: 0.6443 (pmtt) cc_final: 0.5971 (tttp) REVERT: C 95 ASP cc_start: 0.7850 (t0) cc_final: 0.7454 (t70) REVERT: C 127 GLN cc_start: 0.8516 (mm-40) cc_final: 0.7991 (mp10) REVERT: C 256 ASN cc_start: 0.8466 (p0) cc_final: 0.8238 (p0) REVERT: M 32 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7969 (ttmt) REVERT: M 215 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8995 (t80) REVERT: H 51 LYS cc_start: 0.7958 (ptmt) cc_final: 0.7192 (ptpt) REVERT: H 108 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.7280 (t0) REVERT: H 121 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6277 (pt0) REVERT: B 7 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.5983 (pt) REVERT: B 22 PHE cc_start: 0.8118 (t80) cc_final: 0.7851 (t80) REVERT: E 13 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7240 (mp0) REVERT: N 20 ARG cc_start: 0.7825 (mtp-110) cc_final: 0.7527 (mtp85) REVERT: T 20 ARG cc_start: 0.7189 (mtm110) cc_final: 0.6785 (mtm110) REVERT: U 12 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5630 (tp30) REVERT: W 17 ASP cc_start: 0.6899 (t0) cc_final: 0.6606 (t70) REVERT: W 20 ARG cc_start: 0.7981 (mtt90) cc_final: 0.7689 (mtp85) REVERT: 2 33 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8081 (mp) REVERT: 6 53 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6988 (ptt-90) REVERT: 7 12 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: 0 12 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6319 (tt0) REVERT: 0 14 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6862 (mm-30) REVERT: d 18 TRP cc_start: 0.8027 (m100) cc_final: 0.7350 (m100) REVERT: e 17 ASP cc_start: 0.7251 (t0) cc_final: 0.6942 (t0) REVERT: i 12 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5712 (mp0) REVERT: j 12 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7811 (pp) REVERT: n 20 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7697 (ttm110) REVERT: p 18 TRP cc_start: 0.7652 (m100) cc_final: 0.7429 (m100) outliers start: 48 outliers final: 21 residues processed: 370 average time/residue: 0.7602 time to fit residues: 331.3937 Evaluate side-chains 339 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 306 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 32 LYS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 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 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 U residue 12 GLU Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain i residue 12 GLU Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain n residue 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: 9.9990 chunk 234 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 173 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 246 optimal weight: 0.7980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3410 r_free = 0.3410 target = 0.123211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.098066 restraints weight = 32076.423| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 0.93 r_work: 0.2835 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.374 33787 Z= 0.209 Angle : 0.843 14.439 46515 Z= 0.368 Chirality : 0.046 0.188 4813 Planarity : 0.005 0.061 5557 Dihedral : 19.000 179.526 6283 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.51 % Allowed : 8.61 % Favored : 89.88 % 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 are not related in a simple way. whole: 1.57 (0.14), residues: 3355 helix: 1.50 (0.12), residues: 1934 sheet: 0.06 (1.16), residues: 20 loop : 0.58 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 9 19 TYR 0.021 0.003 TYR C 225 PHE 0.024 0.002 PHE L 146 TRP 0.031 0.002 TRP G 30 HIS 0.012 0.002 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (33753) covalent geometry : angle 0.84292 / 0.37 (46515) hydrogen bonds : bond 0.06447 / 4.44 ( 1600) hydrogen bonds : angle 5.07473 / 3.69 ( 4428) Misc. bond : bond 0.10364 / 6.42 ( 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 356 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 312 time to evaluate : 1.284 Fit side-chains REVERT: C 46 LYS cc_start: 0.6563 (pmtt) cc_final: 0.6053 (tttp) REVERT: C 95 ASP cc_start: 0.7808 (t0) cc_final: 0.7425 (t70) REVERT: C 127 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8165 (mp-120) REVERT: C 256 ASN cc_start: 0.8533 (p0) cc_final: 0.8293 (p0) REVERT: M 32 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7899 (ttmt) REVERT: H 51 LYS cc_start: 0.7953 (ptmt) cc_final: 0.7180 (ptpt) REVERT: H 108 ASN cc_start: 0.7619 (OUTLIER) cc_final: 0.7346 (t0) REVERT: H 121 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6404 (pt0) REVERT: B 7 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6054 (pt) REVERT: B 22 PHE cc_start: 0.8078 (t80) cc_final: 0.7784 (t80) REVERT: E 13 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7316 (mp0) REVERT: J 14 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: U 12 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5748 (tp30) REVERT: W 17 ASP cc_start: 0.7139 (t0) cc_final: 0.6716 (t70) REVERT: X 12 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6040 (tp30) REVERT: 2 33 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8015 (mp) REVERT: 6 53 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6989 (ptt-90) REVERT: 7 12 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6904 (mt-10) REVERT: 0 14 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6825 (mm-30) REVERT: j 12 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7832 (pp) REVERT: n 20 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7596 (ttm110) outliers start: 44 outliers final: 21 residues processed: 342 average time/residue: 0.7449 time to fit residues: 299.5232 Evaluate side-chains 330 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 32 LYS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 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 U residue 12 GLU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain j residue 12 ILE Chi-restraints excluded: chain n residue 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: 10.0000 chunk 221 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 165 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3398 r_free = 0.3398 target = 0.122285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.097534 restraints weight = 32069.985| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 0.86 r_work: 0.2834 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.410 33787 Z= 0.224 Angle : 0.876 15.805 46515 Z= 0.382 Chirality : 0.047 0.197 4813 Planarity : 0.006 0.061 5557 Dihedral : 19.340 176.515 6283 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.65 % Allowed : 8.71 % Favored : 89.64 % 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 are not related in a simple way. whole: 1.40 (0.14), residues: 3355 helix: 1.35 (0.12), residues: 1934 sheet: -0.39 (0.84), residues: 32 loop : 0.53 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 9 19 TYR 0.022 0.003 TYR L 164 PHE 0.027 0.003 PHE C 188 TRP 0.031 0.003 TRP G 30 HIS 0.014 0.002 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (33753) covalent geometry : angle 0.87591 / 0.38 (46515) hydrogen bonds : bond 0.06635 / 4.57 ( 1600) hydrogen bonds : angle 5.15703 / 3.75 ( 4428) Misc. bond : bond 0.10782 / 6.64 ( 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 350 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 302 time to evaluate : 1.284 Fit side-chains REVERT: C 95 ASP cc_start: 0.7799 (t0) cc_final: 0.7413 (t70) REVERT: C 127 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8170 (mp-120) REVERT: C 256 ASN cc_start: 0.8534 (p0) cc_final: 0.8308 (p0) REVERT: M 17 HIS cc_start: 0.6117 (p-80) cc_final: 0.5861 (p90) REVERT: M 32 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7893 (ttmt) REVERT: M 215 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8731 (t80) REVERT: H 51 LYS cc_start: 0.7947 (ptmt) cc_final: 0.7187 (ptpt) REVERT: H 108 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7408 (t0) REVERT: H 121 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6288 (pt0) REVERT: A 17 ASP cc_start: 0.7385 (t0) cc_final: 0.7137 (t0) REVERT: B 7 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6071 (pt) REVERT: B 22 PHE cc_start: 0.8087 (t80) cc_final: 0.7798 (t80) REVERT: E 13 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7301 (mp0) REVERT: J 14 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: U 12 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.6057 (mm-30) REVERT: W 17 ASP cc_start: 0.7067 (t0) cc_final: 0.6685 (t70) REVERT: X 12 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6080 (tp30) REVERT: 2 33 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8025 (mp) REVERT: 7 12 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6899 (mt-10) REVERT: 0 14 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6821 (mm-30) REVERT: h 20 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7826 (ttp80) REVERT: j 12 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7879 (pp) REVERT: n 20 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7617 (ttm110) REVERT: o 13 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6484 (mt-10) outliers start: 48 outliers final: 28 residues processed: 336 average time/residue: 0.7634 time to fit residues: 299.3826 Evaluate side-chains 338 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 32 LYS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 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 B residue 32 THR 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 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 12 GLU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain 0 residue 16 LYS Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 20 ARG Chi-restraints excluded: chain j residue 12 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 168 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 229 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3384 r_free = 0.3384 target = 0.121129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.097012 restraints weight = 32050.643| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 0.88 r_work: 0.2819 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.442 33787 Z= 0.303 Angle : 1.009 17.069 46515 Z= 0.439 Chirality : 0.053 0.279 4813 Planarity : 0.007 0.088 5557 Dihedral : 19.728 172.942 6283 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.58 % Allowed : 8.92 % Favored : 89.50 % 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 are not related in a simple way. whole: 1.09 (0.14), residues: 3355 helix: 1.08 (0.11), residues: 1939 sheet: -0.49 (0.83), residues: 32 loop : 0.42 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG h 19 TYR 0.025 0.003 TYR L 164 PHE 0.031 0.003 PHE L 34 TRP 0.032 0.003 TRP G 30 HIS 0.017 0.003 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.30 (33753) covalent geometry : angle 1.00923 / 0.44 (46515) hydrogen bonds : bond 0.07452 / 5.13 ( 1600) hydrogen bonds : angle 5.37378 / 3.90 ( 4428) Misc. bond : bond 0.11116 / 6.86 ( 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 349 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 303 time to evaluate : 1.163 Fit side-chains REVERT: C 46 LYS cc_start: 0.6644 (pmtt) cc_final: 0.6132 (tttp) REVERT: C 95 ASP cc_start: 0.7845 (t0) cc_final: 0.7554 (t70) REVERT: C 127 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8217 (mp-120) REVERT: C 256 ASN cc_start: 0.8540 (p0) cc_final: 0.8320 (p0) REVERT: M 17 HIS cc_start: 0.6112 (p-80) cc_final: 0.5857 (p90) REVERT: M 32 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7967 (ttmt) REVERT: H 51 LYS cc_start: 0.7963 (ptmt) cc_final: 0.7221 (ptpt) REVERT: H 108 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7491 (t0) REVERT: H 121 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6489 (pt0) REVERT: B 7 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6311 (pt) REVERT: B 22 PHE cc_start: 0.8100 (t80) cc_final: 0.7844 (t80) REVERT: E 13 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7361 (mp0) REVERT: J 14 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: T 19 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6568 (ttm110) REVERT: U 12 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.6096 (mm-30) REVERT: W 17 ASP cc_start: 0.6985 (t0) cc_final: 0.6616 (t70) REVERT: X 12 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6266 (tp30) REVERT: 1 14 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8005 (pt0) REVERT: 2 33 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8042 (mp) REVERT: 7 12 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: c 10 LEU cc_start: 0.7719 (mp) cc_final: 0.7347 (mt) REVERT: d 33 LEU cc_start: 0.8574 (mt) cc_final: 0.8168 (mt) REVERT: e 17 ASP cc_start: 0.7728 (t0) cc_final: 0.7471 (t0) REVERT: h 20 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7899 (ttp80) REVERT: j 12 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7910 (pp) REVERT: n 20 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7636 (ttm110) REVERT: o 13 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6526 (mt-10) outliers start: 46 outliers final: 27 residues processed: 334 average time/residue: 0.8393 time to fit residues: 326.9284 Evaluate side-chains 337 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 297 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 32 LYS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 32 THR 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 P residue 9 VAL Chi-restraints excluded: chain Q residue 11 LYS Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain T residue 19 ARG Chi-restraints excluded: chain U residue 12 GLU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain 0 residue 16 LYS Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 20 ARG Chi-restraints excluded: chain j residue 12 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 chunk 333 optimal weight: 5.9990 chunk 165 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3423 r_free = 0.3423 target = 0.124075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.097849 restraints weight = 32311.065| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 0.95 r_work: 0.2872 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.402 33787 Z= 0.182 Angle : 0.806 14.889 46515 Z= 0.352 Chirality : 0.044 0.184 4813 Planarity : 0.005 0.046 5557 Dihedral : 19.214 175.533 6283 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.23 % Allowed : 9.50 % Favored : 89.26 % 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 are not related in a simple way. whole: 1.46 (0.14), residues: 3355 helix: 1.42 (0.12), residues: 1934 sheet: -0.14 (1.14), residues: 20 loop : 0.50 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 9 19 TYR 0.020 0.002 TYR C 225 PHE 0.026 0.002 PHE L 146 TRP 0.027 0.002 TRP d 30 HIS 0.009 0.002 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (33753) covalent geometry : angle 0.80628 / 0.35 (46515) hydrogen bonds : bond 0.06105 / 4.20 ( 1600) hydrogen bonds : angle 5.02883 / 3.66 ( 4428) Misc. bond : bond 0.10907 / 6.85 ( 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 335 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 299 time to evaluate : 1.204 Fit side-chains REVERT: C 46 LYS cc_start: 0.6648 (pmtt) cc_final: 0.6084 (tttp) REVERT: C 74 MET cc_start: 0.9028 (mmt) cc_final: 0.8271 (mmt) REVERT: C 95 ASP cc_start: 0.7819 (t0) cc_final: 0.7525 (t70) REVERT: C 127 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8118 (mp-120) REVERT: C 256 ASN cc_start: 0.8515 (p0) cc_final: 0.8283 (p0) REVERT: M 17 HIS cc_start: 0.6090 (p-80) cc_final: 0.5854 (p90) REVERT: M 32 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7929 (ttmt) REVERT: H 51 LYS cc_start: 0.7931 (ptmt) cc_final: 0.7154 (ptpt) REVERT: H 108 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7406 (t0) REVERT: H 121 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6222 (pt0) REVERT: B 7 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6010 (pt) REVERT: B 22 PHE cc_start: 0.8049 (t80) cc_final: 0.7776 (t80) REVERT: E 13 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7232 (mp0) REVERT: J 14 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: W 17 ASP cc_start: 0.7151 (t0) cc_final: 0.6843 (t70) REVERT: W 20 ARG cc_start: 0.8033 (mtt90) cc_final: 0.7563 (mtp85) REVERT: X 12 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6001 (tp30) REVERT: 1 14 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7973 (pt0) REVERT: 2 33 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7993 (mp) REVERT: 7 12 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6839 (mt-10) REVERT: 0 14 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6839 (mm-30) REVERT: h 17 ASP cc_start: 0.7346 (t0) cc_final: 0.7145 (t0) REVERT: h 20 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7852 (ttt90) REVERT: i 12 GLU cc_start: 0.6530 (tp30) cc_final: 0.6238 (tp30) REVERT: j 12 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7853 (pp) REVERT: n 20 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7555 (ttm110) outliers start: 36 outliers final: 24 residues processed: 324 average time/residue: 0.8275 time to fit residues: 312.6705 Evaluate side-chains 330 residues out of total 2915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 296 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 32 LYS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 288 THR Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain H residue 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 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 Y residue 7 SER Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 6 residue 53 ARG Chi-restraints excluded: chain 7 residue 12 GLU Chi-restraints excluded: chain 0 residue 12 GLU Chi-restraints excluded: chain 0 residue 16 LYS Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 20 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 7 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 329 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 140 optimal weight: 0.0470 chunk 254 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 overall best weight: 1.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 50 GLN C 295 GLN H 82 ASN ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.099954 restraints weight = 32183.483| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 0.92 r_work: 0.2865 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.370 33787 Z= 0.169 Angle : 0.776 14.103 46515 Z= 0.338 Chirality : 0.043 0.183 4813 Planarity : 0.005 0.045 5557 Dihedral : 18.818 174.658 6283 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.34 % Allowed : 9.37 % Favored : 89.30 % 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 are not related in a simple way. whole: 1.57 (0.14), residues: 3355 helix: 1.51 (0.12), residues: 1934 sheet: -0.11 (1.16), residues: 20 loop : 0.55 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 9 19 TYR 0.022 0.002 TYR j 1 PHE 0.026 0.002 PHE M 215 TRP 0.027 0.002 TRP d 30 HIS 0.008 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (33753) covalent geometry : angle 0.77560 / 0.34 (46515) hydrogen bonds : bond 0.05854 / 4.02 ( 1600) hydrogen bonds : angle 4.94790 / 3.60 ( 4428) Misc. bond : bond 0.10397 / 6.59 ( 34) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13367.09 seconds wall clock time: 228 minutes 1.92 seconds (13681.92 seconds total)