Starting phenix.real_space_refine on Thu Jun 19 19:50:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7voy_32062/06_2025/7voy_32062.cif Found real_map, /net/cci-nas-00/data/ceres_data/7voy_32062/06_2025/7voy_32062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7voy_32062/06_2025/7voy_32062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7voy_32062/06_2025/7voy_32062.map" model { file = "/net/cci-nas-00/data/ceres_data/7voy_32062/06_2025/7voy_32062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7voy_32062/06_2025/7voy_32062.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 Mg 38 5.21 5 S 96 5.16 5 C 15044 2.51 5 N 3398 2.21 5 O 3542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22119 Number of models: 1 Model: "" Number of chains: 71 Chain: "A" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "U" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "V" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "W" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "X" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Y" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "Z" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "2" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "7" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "8" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "0" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "4" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "t" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "6" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "5" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "C" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "3" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2431 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "H" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1875 Classifications: {'peptide': 247} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 223} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "Q" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "T" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "U" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "V" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "W" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "X" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "Y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "1" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "2" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "7" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "8" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "9" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "0" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "t" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "5" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "3" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'BCL': 1, 'BPH': 1, 'U10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'BCL:plan_0002': 1, 'BPH:plan-1': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-11': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-2': 1, 'U10:plan-3': 1} Unresolved non-hydrogen planarities: 51 Chain: "M" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 241 Unusual residues: {'BCL': 3, 'BPH': 1, 'FE2': 1, 'SPN': 1, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'BCL:plan_0002': 3, 'BPH:plan-1': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-11': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-2': 1, 'U10:plan-3': 1} Unresolved non-hydrogen planarities: 63 Time building chain proxies: 12.76, per 1000 atoms: 0.58 Number of scatterers: 22119 At special positions: 0 Unit cell: (139.92, 137.8, 119.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 1 26.01 S 96 16.00 Mg 38 11.99 O 3542 8.00 N 3398 7.00 C 15044 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 2.4 seconds 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4638 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 6 sheets defined 72.3% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.976A pdb=" N MET A 9 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.579A pdb=" N VAL A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'B' and resid 13 through 46 Processing helix chain 'D' and resid 5 through 11 removed outlier: 4.003A pdb=" N MET D 9 " --> pdb=" O TYR D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 38 Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'E' and resid 13 through 46 Processing helix chain 'F' and resid 4 through 11 Processing helix chain 'F' and resid 12 through 38 removed outlier: 3.922A pdb=" N PHE F 17 " --> pdb=" O PRO F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'G' and resid 13 through 46 Processing helix chain 'I' and resid 2 through 10 removed outlier: 4.279A pdb=" N TYR I 5 " --> pdb=" O SER I 2 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE I 7 " --> pdb=" O PHE I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 38 Processing helix chain 'I' and resid 42 through 51 Processing helix chain 'J' and resid 13 through 46 Processing helix chain 'K' and resid 3 through 5 No H-bonds generated for 'chain 'K' and resid 3 through 5' Processing helix chain 'K' and resid 6 through 11 Processing helix chain 'K' and resid 12 through 37 Processing helix chain 'K' and resid 42 through 52 Processing helix chain 'N' and resid 13 through 46 Processing helix chain 'O' and resid 2 through 10 removed outlier: 4.410A pdb=" N TYR O 5 " --> pdb=" O SER O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 38 Processing helix chain 'O' and resid 42 through 51 Processing helix chain 'P' and resid 13 through 46 Processing helix chain 'Q' and resid 3 through 10 removed outlier: 3.650A pdb=" N LYS Q 6 " --> pdb=" O LYS Q 3 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP Q 8 " --> pdb=" O TYR Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 38 removed outlier: 3.944A pdb=" N THR Q 38 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 51 Processing helix chain 'R' and resid 13 through 46 Processing helix chain 'S' and resid 6 through 11 removed outlier: 3.986A pdb=" N ILE S 10 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE S 11 " --> pdb=" O ILE S 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 6 through 11' Processing helix chain 'S' and resid 12 through 38 Processing helix chain 'S' and resid 42 through 51 Processing helix chain 'T' and resid 13 through 46 Processing helix chain 'U' and resid 3 through 10 Processing helix chain 'U' and resid 12 through 38 removed outlier: 3.570A pdb=" N THR U 38 " --> pdb=" O ILE U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 51 Processing helix chain 'V' and resid 13 through 46 Processing helix chain 'W' and resid 3 through 5 No H-bonds generated for 'chain 'W' and resid 3 through 5' Processing helix chain 'W' and resid 6 through 11 removed outlier: 3.838A pdb=" N ILE W 10 " --> pdb=" O LYS W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 38 Processing helix chain 'W' and resid 42 through 52 Processing helix chain 'X' and resid 13 through 46 Processing helix chain 'Y' and resid 1 through 4 Processing helix chain 'Y' and resid 5 through 11 Processing helix chain 'Y' and resid 12 through 38 removed outlier: 3.558A pdb=" N VAL Y 16 " --> pdb=" O ASP Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 51 Processing helix chain 'Z' and resid 13 through 46 Processing helix chain '1' and resid 6 through 11 removed outlier: 3.929A pdb=" N ILE 1 10 " --> pdb=" O LYS 1 6 " (cutoff:3.500A) Processing helix chain '1' and resid 12 through 38 removed outlier: 3.709A pdb=" N VAL 1 16 " --> pdb=" O ASP 1 12 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR 1 38 " --> pdb=" O ILE 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 51 Processing helix chain '2' and resid 13 through 46 Processing helix chain '7' and resid 6 through 11 Processing helix chain '7' and resid 12 through 38 Processing helix chain '7' and resid 42 through 46 Processing helix chain '8' and resid 13 through 46 Processing helix chain '9' and resid 1 through 4 removed outlier: 3.717A pdb=" N PHE 9 4 " --> pdb=" O MET 9 1 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 1 through 4' Processing helix chain '9' and resid 5 through 11 removed outlier: 3.847A pdb=" N MET 9 9 " --> pdb=" O TYR 9 5 " (cutoff:3.500A) Processing helix chain '9' and resid 12 through 38 removed outlier: 3.614A pdb=" N VAL 9 16 " --> pdb=" O ASP 9 12 " (cutoff:3.500A) Processing helix chain '9' and resid 42 through 52 Processing helix chain '0' and resid 13 through 46 Processing helix chain '4' and resid 5 through 11 removed outlier: 3.905A pdb=" N MET 4 9 " --> pdb=" O TYR 4 5 " (cutoff:3.500A) Processing helix chain '4' and resid 12 through 38 Processing helix chain '4' and resid 42 through 52 removed outlier: 3.570A pdb=" N ILE 4 46 " --> pdb=" O ASN 4 42 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER 4 47 " --> pdb=" O TRP 4 43 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA 4 48 " --> pdb=" O LEU 4 44 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA 4 49 " --> pdb=" O GLU 4 45 " (cutoff:3.500A) Processing helix chain 't' and resid 13 through 46 Processing helix chain '6' and resid 5 through 11 removed outlier: 4.014A pdb=" N MET 6 9 " --> pdb=" O TYR 6 5 " (cutoff:3.500A) Processing helix chain '6' and resid 12 through 38 Processing helix chain '6' and resid 42 through 52 removed outlier: 3.517A pdb=" N ALA 6 48 " --> pdb=" O LEU 6 44 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS 6 50 " --> pdb=" O ILE 6 46 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR 6 51 " --> pdb=" O SER 6 47 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 46 Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 6 through 11 removed outlier: 3.762A pdb=" N ILE C 10 " --> pdb=" O LYS C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 38 Processing helix chain 'C' and resid 39 through 41 No H-bonds generated for 'chain 'C' and resid 39 through 41' Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.613A pdb=" N SER C 47 " --> pdb=" O TRP C 43 " (cutoff:3.500A) Processing helix chain '3' and resid 13 through 46 Processing helix chain 'L' and resid 6 through 10 Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.749A pdb=" N ALA L 37 " --> pdb=" O PHE L 33 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR L 38 " --> pdb=" O PHE L 34 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE L 39 " --> pdb=" O GLY L 35 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU L 44 " --> pdb=" O PHE L 40 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 47 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE L 49 " --> pdb=" O GLY L 45 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA L 53 " --> pdb=" O ILE L 49 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL L 54 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU L 55 " --> pdb=" O TRP L 51 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN L 56 " --> pdb=" O SER L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 64 removed outlier: 3.821A pdb=" N ILE L 64 " --> pdb=" O PRO L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 112 removed outlier: 3.701A pdb=" N ILE L 91 " --> pdb=" O GLN L 87 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL L 105 " --> pdb=" O ALA L 101 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU L 106 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 130 removed outlier: 3.902A pdb=" N ALA L 127 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR L 128 " --> pdb=" O ALA L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 140 removed outlier: 3.645A pdb=" N MET L 139 " --> pdb=" O ARG L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 145 removed outlier: 3.680A pdb=" N TYR L 144 " --> pdb=" O ALA L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 153 Processing helix chain 'L' and resid 161 through 165 Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 170 through 199 removed outlier: 3.775A pdb=" N SER L 178 " --> pdb=" O MET L 174 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE L 180 " --> pdb=" O ALA L 176 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU L 189 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL L 194 " --> pdb=" O HIS L 190 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU L 195 " --> pdb=" O GLY L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 221 removed outlier: 3.515A pdb=" N GLU L 212 " --> pdb=" O THR L 208 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP L 213 " --> pdb=" O PRO L 209 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR L 214 " --> pdb=" O ASP L 210 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE L 215 " --> pdb=" O HIS L 211 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE L 216 " --> pdb=" O GLU L 212 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU L 219 " --> pdb=" O PHE L 215 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL L 220 " --> pdb=" O PHE L 216 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 250 removed outlier: 3.711A pdb=" N ILE L 229 " --> pdb=" O GLY L 225 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS L 247 " --> pdb=" O PHE L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 268 removed outlier: 4.359A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN L 264 " --> pdb=" O VAL L 260 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP L 265 " --> pdb=" O ASP L 261 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 43 Processing helix chain 'M' and resid 53 through 79 removed outlier: 3.890A pdb=" N ILE M 70 " --> pdb=" O TRP M 66 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY M 71 " --> pdb=" O PHE M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 112 through 141 removed outlier: 3.810A pdb=" N PHE M 121 " --> pdb=" O ILE M 117 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP M 127 " --> pdb=" O PHE M 123 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP M 130 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY M 131 " --> pdb=" O TRP M 127 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG M 132 " --> pdb=" O SER M 128 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG M 136 " --> pdb=" O ARG M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.772A pdb=" N PHE M 150 " --> pdb=" O THR M 146 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU M 156 " --> pdb=" O SER M 152 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY M 161 " --> pdb=" O TRP M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 169 removed outlier: 3.881A pdb=" N MET M 168 " --> pdb=" O ARG M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 193 removed outlier: 3.714A pdb=" N SER M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 226 removed outlier: 3.670A pdb=" N ALA M 207 " --> pdb=" O GLY M 203 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE M 208 " --> pdb=" O LEU M 204 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR M 210 " --> pdb=" O ILE M 206 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA M 213 " --> pdb=" O LEU M 209 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 238 removed outlier: 3.913A pdb=" N ILE M 238 " --> pdb=" O LEU M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 257 removed outlier: 4.313A pdb=" N ALA M 248 " --> pdb=" O ALA M 244 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA M 249 " --> pdb=" O ALA M 245 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU M 250 " --> pdb=" O GLU M 246 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE M 251 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 290 removed outlier: 4.065A pdb=" N HIS M 266 " --> pdb=" O MET M 262 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG M 267 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP M 268 " --> pdb=" O GLY M 264 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA M 269 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE M 270 " --> pdb=" O HIS M 266 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU M 275 " --> pdb=" O TRP M 271 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR M 279 " --> pdb=" O LEU M 275 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY M 280 " --> pdb=" O VAL M 276 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE M 282 " --> pdb=" O LEU M 278 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU M 285 " --> pdb=" O GLY M 281 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU M 286 " --> pdb=" O ILE M 282 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER M 287 " --> pdb=" O GLY M 283 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY M 288 " --> pdb=" O ILE M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 298 Processing helix chain 'M' and resid 299 through 302 removed outlier: 3.655A pdb=" N GLY M 302 " --> pdb=" O GLN M 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 299 through 302' Processing helix chain 'H' and resid 11 through 35 removed outlier: 3.692A pdb=" N ILE H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 108 removed outlier: 3.659A pdb=" N ASP H 107 " --> pdb=" O ASP H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 113 removed outlier: 4.074A pdb=" N SER H 113 " --> pdb=" O GLY H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 214 removed outlier: 3.788A pdb=" N ALA H 214 " --> pdb=" O SER H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 244 removed outlier: 3.786A pdb=" N ASP H 231 " --> pdb=" O LEU H 227 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY H 240 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR H 243 " --> pdb=" O GLY H 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'M' and resid 93 through 94 Processing sheet with id=AA3, first strand: chain 'H' and resid 63 through 65 removed outlier: 4.196A pdb=" N LEU H 73 " --> pdb=" O PHE H 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.559A pdb=" N VAL H 164 " --> pdb=" O GLU H 182 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLU H 182 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP H 166 " --> pdb=" O GLU H 180 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASP H 170 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ALA H 176 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 131 through 133 removed outlier: 4.023A pdb=" N VAL H 203 " --> pdb=" O PRO H 152 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N HIS H 204 " --> pdb=" O LYS H 197 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS H 197 " --> pdb=" O HIS H 204 " (cutoff:3.500A) 1288 hydrogen bonds defined for protein. 3765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 7.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.35: 6296 1.35 - 1.56: 16463 1.56 - 1.76: 21 1.76 - 1.97: 187 1.97 - 2.17: 152 Bond restraints: 23119 Sorted by residual: bond pdb=" C29 SPN M 407 " pdb=" C30 SPN M 407 " ideal model delta sigma weight residual 1.336 1.545 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C8 SPN M 407 " pdb=" C9 SPN M 407 " ideal model delta sigma weight residual 1.336 1.533 -0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" C14 SPN M 407 " pdb=" C15 SPN M 407 " ideal model delta sigma weight residual 1.530 1.336 0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" C16 SPN M 407 " pdb=" C17 SPN M 407 " ideal model delta sigma weight residual 1.530 1.344 0.186 2.00e-02 2.50e+03 8.66e+01 bond pdb=" C26 SPN M 407 " pdb=" CM8 SPN M 407 " ideal model delta sigma weight residual 1.502 1.318 0.184 2.00e-02 2.50e+03 8.45e+01 ... (remaining 23114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.81: 32168 9.81 - 19.62: 11 19.62 - 29.42: 0 29.42 - 39.23: 2 39.23 - 49.04: 1 Bond angle restraints: 32182 Sorted by residual: angle pdb=" C3B BCL E 101 " pdb=" CAB BCL E 101 " pdb=" OBB BCL E 101 " ideal model delta sigma weight residual 122.70 73.66 49.04 2.78e+00 1.29e-01 3.10e+02 angle pdb=" CBB BCL E 101 " pdb=" CAB BCL E 101 " pdb=" OBB BCL E 101 " ideal model delta sigma weight residual 116.79 80.19 36.60 2.39e+00 1.75e-01 2.34e+02 angle pdb=" C3B BCL E 101 " pdb=" CAB BCL E 101 " pdb=" CBB BCL E 101 " ideal model delta sigma weight residual 120.43 153.85 -33.42 2.41e+00 1.73e-01 1.93e+02 angle pdb=" C TYR 0 9 " pdb=" N THR 0 10 " pdb=" CA THR 0 10 " ideal model delta sigma weight residual 121.92 106.03 15.89 1.73e+00 3.34e-01 8.44e+01 angle pdb=" C TYR 3 9 " pdb=" N THR 3 10 " pdb=" CA THR 3 10 " ideal model delta sigma weight residual 122.24 110.42 11.82 1.57e+00 4.06e-01 5.67e+01 ... (remaining 32177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.83: 11029 18.83 - 37.65: 811 37.65 - 56.48: 180 56.48 - 75.31: 36 75.31 - 94.13: 28 Dihedral angle restraints: 12084 sinusoidal: 4877 harmonic: 7207 Sorted by residual: dihedral pdb=" CA TYR V 9 " pdb=" C TYR V 9 " pdb=" N THR V 10 " pdb=" CA THR V 10 " ideal model delta harmonic sigma weight residual 180.00 140.79 39.21 0 5.00e+00 4.00e-02 6.15e+01 dihedral pdb=" CA TYR 0 9 " pdb=" C TYR 0 9 " pdb=" N THR 0 10 " pdb=" CA THR 0 10 " ideal model delta harmonic sigma weight residual -180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA TYR P 9 " pdb=" C TYR P 9 " pdb=" N THR P 10 " pdb=" CA THR P 10 " ideal model delta harmonic sigma weight residual 180.00 144.80 35.20 0 5.00e+00 4.00e-02 4.96e+01 ... (remaining 12081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.048: 3296 1.048 - 2.096: 0 2.096 - 3.144: 0 3.144 - 4.192: 0 4.192 - 5.240: 1 Chirality restraints: 3297 Sorted by residual: chirality pdb=" C22 SPN M 407 " pdb=" C21 SPN M 407 " pdb=" C23 SPN M 407 " pdb=" CM7 SPN M 407 " both_signs ideal model delta sigma weight residual False -2.58 2.66 -5.24 2.00e-01 2.50e+01 6.86e+02 chirality pdb=" C3C BPH M 405 " pdb=" C2C BPH M 405 " pdb=" C4C BPH M 405 " pdb=" CAC BPH M 405 " both_signs ideal model delta sigma weight residual False 2.83 2.60 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA TYR P 9 " pdb=" N TYR P 9 " pdb=" C TYR P 9 " pdb=" CB TYR P 9 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3294 not shown) Planarity restraints: 3861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 SPN M 407 " -0.176 2.00e-02 2.50e+03 2.26e-01 6.41e+02 pdb=" C29 SPN M 407 " 0.345 2.00e-02 2.50e+03 pdb=" C30 SPN M 407 " -0.289 2.00e-02 2.50e+03 pdb=" CM9 SPN M 407 " 0.150 2.00e-02 2.50e+03 pdb=" CMB SPN M 407 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 SPN M 407 " -0.094 2.00e-02 2.50e+03 1.68e-01 3.51e+02 pdb=" C7 SPN M 407 " 0.021 2.00e-02 2.50e+03 pdb=" C8 SPN M 407 " -0.132 2.00e-02 2.50e+03 pdb=" C9 SPN M 407 " 0.318 2.00e-02 2.50e+03 pdb=" CM4 SPN M 407 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH M 405 " -0.020 2.00e-02 2.50e+03 1.12e-01 2.80e+02 pdb=" C1D BPH M 405 " -0.029 2.00e-02 2.50e+03 pdb=" C2D BPH M 405 " 0.055 2.00e-02 2.50e+03 pdb=" C3D BPH M 405 " 0.088 2.00e-02 2.50e+03 pdb=" C4D BPH M 405 " 0.071 2.00e-02 2.50e+03 pdb=" CAD BPH M 405 " -0.250 2.00e-02 2.50e+03 pdb=" CHA BPH M 405 " 0.095 2.00e-02 2.50e+03 pdb=" CHD BPH M 405 " -0.113 2.00e-02 2.50e+03 pdb=" CMD BPH M 405 " 0.104 2.00e-02 2.50e+03 ... (remaining 3858 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 302 2.62 - 3.19: 20720 3.19 - 3.76: 36412 3.76 - 4.33: 47449 4.33 - 4.90: 76475 Nonbonded interactions: 181358 Sorted by model distance: nonbonded pdb=" OG1 THR K 38 " pdb=" O SER K 40 " model vdw 2.056 3.040 nonbonded pdb=" OG1 THR L 15 " pdb=" O GLY L 18 " model vdw 2.063 3.040 nonbonded pdb=" O TRP R 48 " pdb=" OG SER S 47 " model vdw 2.066 3.040 nonbonded pdb=" O PRO V 47 " pdb=" NH2 ARG W 53 " model vdw 2.094 3.120 nonbonded pdb=" O TYR L 30 " pdb=" NH2 ARG L 103 " model vdw 2.118 3.120 ... (remaining 181353 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 10 through 49 or resid 101)) selection = chain '2' selection = (chain '3' and (resid 10 through 49 or resid 101)) selection = (chain '5' and (resid 10 through 49 or resid 101)) selection = (chain '8' and (resid 10 through 49 or resid 101)) selection = (chain 'B' and (resid 10 through 49 or resid 101)) selection = (chain 'E' and (resid 10 through 49 or resid 101)) selection = (chain 'G' and (resid 10 through 49 or resid 101)) selection = (chain 'J' and (resid 10 through 49 or resid 101)) selection = (chain 'N' and (resid 10 through 49 or resid 101)) selection = (chain 'P' and (resid 10 through 49 or resid 101)) selection = (chain 'R' and (resid 10 through 49 or resid 101)) selection = (chain 'T' and (resid 10 through 49 or resid 101)) selection = (chain 'V' and (resid 10 through 49 or resid 101)) selection = (chain 'X' and (resid 10 through 49 or resid 101)) selection = (chain 'Z' and (resid 10 through 49 or resid 101)) selection = (chain 't' and (resid 10 through 49 or resid 101)) } ncs_group { reference = (chain '1' and resid 2 through 46) selection = (chain '4' and resid 2 through 46) selection = (chain '6' and resid 2 through 46) selection = (chain '7' and resid 2 through 46) selection = (chain '9' and resid 2 through 46) selection = (chain 'A' and resid 2 through 46) selection = (chain 'C' and resid 2 through 46) selection = (chain 'D' and resid 2 through 46) selection = (chain 'F' and resid 2 through 46) selection = (chain 'I' and resid 2 through 46) selection = (chain 'K' and resid 2 through 46) selection = (chain 'O' and resid 2 through 46) selection = (chain 'Q' and resid 2 through 46) selection = (chain 'S' and resid 2 through 46) selection = (chain 'U' and resid 2 through 46) selection = (chain 'W' and resid 2 through 46) selection = (chain 'Y' and resid 2 through 46) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 45.960 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 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 : 0.017 0.691 23139 Z= 1.563 Angle : 0.975 49.038 32182 Z= 0.454 Chirality : 0.101 5.240 3297 Planarity : 0.008 0.226 3861 Dihedral : 14.581 94.135 7446 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.38 % Rotamer: Outliers : 1.25 % Allowed : 4.41 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2405 helix: 1.72 (0.13), residues: 1501 sheet: -2.51 (0.84), residues: 22 loop : -1.15 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Y 8 HIS 0.006 0.001 HIS M 266 PHE 0.024 0.002 PHE Q 11 TYR 0.028 0.002 TYR 3 9 ARG 0.006 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.18077 ( 1286) hydrogen bonds : angle 6.28482 ( 3765) covalent geometry : bond 0.00870 (23119) covalent geometry : angle 0.97475 (32182) Misc. bond : bond 0.51459 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 865 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 THR cc_start: 0.3925 (p) cc_final: 0.3619 (p) REVERT: B 16 GLN cc_start: 0.7510 (mt0) cc_final: 0.7186 (mt0) REVERT: F 12 ASP cc_start: 0.8225 (t0) cc_final: 0.7907 (t0) REVERT: G 29 TRP cc_start: 0.8038 (m100) cc_final: 0.7631 (m100) REVERT: G 43 TYR cc_start: 0.8078 (t80) cc_final: 0.6945 (t80) REVERT: I 42 ASN cc_start: 0.8056 (t0) cc_final: 0.7730 (t0) REVERT: J 16 GLN cc_start: 0.6962 (mt0) cc_final: 0.6379 (mm110) REVERT: J 21 HIS cc_start: 0.8479 (t70) cc_final: 0.7723 (t70) REVERT: J 29 TRP cc_start: 0.7827 (m100) cc_final: 0.7450 (m-10) REVERT: K 50 LYS cc_start: 0.7740 (tttt) cc_final: 0.7483 (ttpt) REVERT: O 15 ARG cc_start: 0.6181 (ttp-170) cc_final: 0.4457 (ttp80) REVERT: O 39 PRO cc_start: 0.8616 (Cg_exo) cc_final: 0.8313 (Cg_endo) REVERT: Q 1 MET cc_start: 0.3661 (ptt) cc_final: 0.3216 (ttp) REVERT: Q 7 ILE cc_start: 0.7347 (mm) cc_final: 0.7041 (mm) REVERT: Q 35 LEU cc_start: 0.9244 (mp) cc_final: 0.8989 (mp) REVERT: R 12 LEU cc_start: 0.8810 (mp) cc_final: 0.8421 (mp) REVERT: S 34 ILE cc_start: 0.9057 (mt) cc_final: 0.8754 (mm) REVERT: T 10 THR cc_start: 0.6822 (p) cc_final: 0.6520 (p) REVERT: W 43 TRP cc_start: 0.8344 (p90) cc_final: 0.7917 (p90) REVERT: X 42 VAL cc_start: 0.8708 (t) cc_final: 0.8438 (p) REVERT: Y 30 MET cc_start: 0.8167 (ttp) cc_final: 0.7709 (ttt) REVERT: Z 16 GLN cc_start: 0.6422 (mt0) cc_final: 0.5992 (mt0) REVERT: Z 29 TRP cc_start: 0.7944 (m100) cc_final: 0.7465 (m100) REVERT: 1 9 MET cc_start: 0.5943 (ptp) cc_final: 0.4696 (ttt) REVERT: 1 14 ARG cc_start: 0.7281 (mpt-90) cc_final: 0.7043 (ptp-170) REVERT: 2 13 THR cc_start: 0.7550 (p) cc_final: 0.7269 (p) REVERT: 2 14 ASP cc_start: 0.6785 (m-30) cc_final: 0.6192 (m-30) REVERT: 2 24 TYR cc_start: 0.7778 (t80) cc_final: 0.7532 (t80) REVERT: 7 14 ARG cc_start: 0.8024 (mtm180) cc_final: 0.7673 (mtp180) REVERT: 7 24 LEU cc_start: 0.7966 (mt) cc_final: 0.7735 (mt) REVERT: 8 18 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7094 (tm-30) REVERT: 8 29 TRP cc_start: 0.7471 (m100) cc_final: 0.7042 (m100) REVERT: 0 39 HIS cc_start: 0.6810 (m90) cc_final: 0.6324 (m90) REVERT: 0 42 VAL cc_start: 0.9325 (t) cc_final: 0.9031 (p) REVERT: 4 9 MET cc_start: 0.6555 (tpt) cc_final: 0.5894 (tpt) REVERT: t 13 THR cc_start: 0.6909 (p) cc_final: 0.6624 (p) REVERT: t 15 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6449 (mt-10) REVERT: t 18 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7088 (mt0) REVERT: t 24 TYR cc_start: 0.7598 (t80) cc_final: 0.7190 (t80) REVERT: t 29 TRP cc_start: 0.7143 (m100) cc_final: 0.6822 (m100) REVERT: t 46 ARG cc_start: 0.6905 (ttm170) cc_final: 0.5396 (tpt-90) REVERT: 6 5 TYR cc_start: 0.6837 (p90) cc_final: 0.6400 (p90) REVERT: 5 21 HIS cc_start: 0.8323 (t70) cc_final: 0.7953 (t-170) REVERT: C 3 LYS cc_start: 0.8110 (mptt) cc_final: 0.7655 (mmmt) REVERT: C 6 LYS cc_start: 0.7628 (mppt) cc_final: 0.6611 (mmmt) REVERT: C 15 ARG cc_start: 0.6013 (mmt180) cc_final: 0.5351 (mmm160) REVERT: C 46 ILE cc_start: 0.8051 (mp) cc_final: 0.7658 (mt) REVERT: 3 15 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: 3 25 MET cc_start: 0.7582 (mmm) cc_final: 0.7193 (tpp) REVERT: L 91 ILE cc_start: 0.4555 (mt) cc_final: 0.3992 (tp) REVERT: M 18 LEU cc_start: 0.5806 (mt) cc_final: 0.5379 (mt) REVERT: M 65 MET cc_start: 0.2725 (tpp) cc_final: 0.2493 (tpp) REVERT: M 144 LYS cc_start: 0.3030 (mppt) cc_final: 0.2629 (mmpt) REVERT: M 184 ASP cc_start: 0.5331 (t0) cc_final: 0.5069 (t0) REVERT: M 235 LEU cc_start: 0.5340 (tp) cc_final: 0.4762 (tp) REVERT: M 236 GLU cc_start: 0.4928 (mp0) cc_final: 0.4402 (pm20) REVERT: M 272 MET cc_start: 0.3477 (ttm) cc_final: 0.2948 (tpp) outliers start: 26 outliers final: 2 residues processed: 877 average time/residue: 0.3197 time to fit residues: 441.3234 Evaluate side-chains 715 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 711 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 5.9990 chunk 177 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 212 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN W 20 GLN 1 20 GLN 0 16 GLN 6 52 ASN C 20 GLN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.186436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143582 restraints weight = 41242.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.146812 restraints weight = 21453.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.148793 restraints weight = 14565.461| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23139 Z= 0.152 Angle : 0.747 47.950 32182 Z= 0.352 Chirality : 0.041 0.255 3297 Planarity : 0.005 0.071 3861 Dihedral : 9.289 89.997 3057 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.34 % Allowed : 4.46 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.17), residues: 2405 helix: 2.10 (0.13), residues: 1541 sheet: -1.84 (0.99), residues: 20 loop : -0.97 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 156 HIS 0.008 0.002 HIS L 211 PHE 0.033 0.002 PHE 1 11 TYR 0.017 0.002 TYR W 5 ARG 0.007 0.001 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.05322 ( 1286) hydrogen bonds : angle 4.36193 ( 3765) covalent geometry : bond 0.00328 (23119) covalent geometry : angle 0.74729 (32182) Misc. bond : bond 0.00104 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 818 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.7559 (m-10) cc_final: 0.7328 (m-10) REVERT: A 14 ARG cc_start: 0.6590 (ptp90) cc_final: 0.6145 (mtm180) REVERT: A 40 SER cc_start: 0.7347 (p) cc_final: 0.6800 (t) REVERT: A 51 TYR cc_start: 0.6559 (m-10) cc_final: 0.6208 (m-10) REVERT: A 52 ASN cc_start: 0.6771 (m-40) cc_final: 0.5668 (t0) REVERT: B 14 ASP cc_start: 0.6012 (t0) cc_final: 0.5710 (t0) REVERT: B 21 HIS cc_start: 0.8264 (t-90) cc_final: 0.8030 (t-90) REVERT: F 30 MET cc_start: 0.8094 (tmm) cc_final: 0.7876 (tmm) REVERT: G 24 TYR cc_start: 0.7520 (t80) cc_final: 0.7257 (t80) REVERT: G 29 TRP cc_start: 0.7956 (m100) cc_final: 0.7750 (m100) REVERT: I 11 PHE cc_start: 0.7923 (m-10) cc_final: 0.7721 (m-10) REVERT: J 12 LEU cc_start: 0.6976 (mm) cc_final: 0.6304 (mm) REVERT: J 16 GLN cc_start: 0.7021 (mt0) cc_final: 0.6435 (mm110) REVERT: J 21 HIS cc_start: 0.8667 (t70) cc_final: 0.7826 (t70) REVERT: J 29 TRP cc_start: 0.8007 (m100) cc_final: 0.7551 (m-10) REVERT: N 15 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7303 (tp30) REVERT: N 25 MET cc_start: 0.8762 (mmm) cc_final: 0.8285 (mmm) REVERT: O 10 ILE cc_start: 0.8217 (mt) cc_final: 0.7971 (mt) REVERT: O 15 ARG cc_start: 0.6260 (ptm-80) cc_final: 0.5556 (mtm110) REVERT: Q 1 MET cc_start: 0.3240 (ptt) cc_final: 0.2871 (ttp) REVERT: Q 7 ILE cc_start: 0.7269 (mm) cc_final: 0.7003 (mm) REVERT: Q 23 PHE cc_start: 0.8414 (t80) cc_final: 0.8166 (t80) REVERT: Q 51 TYR cc_start: 0.8357 (m-80) cc_final: 0.7873 (m-80) REVERT: R 12 LEU cc_start: 0.8759 (mp) cc_final: 0.8418 (mp) REVERT: S 13 PRO cc_start: 0.8192 (Cg_endo) cc_final: 0.7907 (Cg_exo) REVERT: S 34 ILE cc_start: 0.8867 (mt) cc_final: 0.8529 (mm) REVERT: T 15 GLU cc_start: 0.8091 (pt0) cc_final: 0.7770 (tp30) REVERT: T 25 MET cc_start: 0.7967 (mtp) cc_final: 0.7751 (mmm) REVERT: U 6 LYS cc_start: 0.7744 (mttp) cc_final: 0.6981 (mmtm) REVERT: U 12 ASP cc_start: 0.7019 (t70) cc_final: 0.6487 (t70) REVERT: W 43 TRP cc_start: 0.8324 (p90) cc_final: 0.7793 (p90) REVERT: X 14 ASP cc_start: 0.8190 (m-30) cc_final: 0.7912 (m-30) REVERT: X 42 VAL cc_start: 0.8570 (t) cc_final: 0.8266 (p) REVERT: 1 14 ARG cc_start: 0.7420 (mpt-90) cc_final: 0.7188 (ptp-170) REVERT: 2 13 THR cc_start: 0.7644 (p) cc_final: 0.7241 (t) REVERT: 2 14 ASP cc_start: 0.6738 (m-30) cc_final: 0.6430 (m-30) REVERT: 2 20 LEU cc_start: 0.8503 (tp) cc_final: 0.8287 (tp) REVERT: 2 32 SER cc_start: 0.8720 (m) cc_final: 0.8376 (m) REVERT: 7 36 LEU cc_start: 0.8067 (tt) cc_final: 0.7716 (tt) REVERT: 7 42 ASN cc_start: 0.7519 (t0) cc_final: 0.6932 (t0) REVERT: 8 12 LEU cc_start: 0.8084 (mm) cc_final: 0.7500 (mt) REVERT: 8 15 GLU cc_start: 0.7352 (tp30) cc_final: 0.6938 (tp30) REVERT: 8 18 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7124 (tm-30) REVERT: 8 25 MET cc_start: 0.8381 (mmm) cc_final: 0.7786 (mmt) REVERT: 8 29 TRP cc_start: 0.7625 (m100) cc_final: 0.7151 (m100) REVERT: 4 34 ILE cc_start: 0.8766 (mt) cc_final: 0.8299 (tp) REVERT: t 15 GLU cc_start: 0.7578 (mp0) cc_final: 0.7264 (mt-10) REVERT: t 18 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7137 (mt0) REVERT: t 29 TRP cc_start: 0.7307 (m100) cc_final: 0.6890 (m100) REVERT: t 46 ARG cc_start: 0.6597 (ttm170) cc_final: 0.5804 (tpt-90) REVERT: 6 5 TYR cc_start: 0.6134 (p90) cc_final: 0.5826 (p90) REVERT: 5 21 HIS cc_start: 0.8618 (t70) cc_final: 0.8118 (t70) REVERT: 5 42 VAL cc_start: 0.8683 (m) cc_final: 0.8449 (p) REVERT: C 3 LYS cc_start: 0.7973 (mptt) cc_final: 0.7490 (mmtm) REVERT: C 15 ARG cc_start: 0.5861 (mmt180) cc_final: 0.5383 (mmm160) REVERT: C 37 SER cc_start: 0.8704 (m) cc_final: 0.8293 (p) REVERT: L 217 ARG cc_start: 0.4619 (mtp180) cc_final: 0.4293 (mtp180) REVERT: M 18 LEU cc_start: 0.5353 (mt) cc_final: 0.4947 (mt) REVERT: M 236 GLU cc_start: 0.5120 (mp0) cc_final: 0.4748 (pt0) REVERT: M 256 MET cc_start: 0.5996 (mmp) cc_final: 0.5383 (ptm) REVERT: M 272 MET cc_start: 0.2974 (ttm) cc_final: 0.2264 (tpp) REVERT: H 173 GLU cc_start: 0.5320 (mp0) cc_final: 0.4403 (pm20) REVERT: H 175 MET cc_start: 0.3734 (ptt) cc_final: 0.3312 (ptt) outliers start: 7 outliers final: 0 residues processed: 819 average time/residue: 0.3053 time to fit residues: 394.8707 Evaluate side-chains 711 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 711 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 204 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 228 optimal weight: 30.0000 chunk 214 optimal weight: 1.9990 chunk 172 optimal weight: 0.1980 chunk 94 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 20 GLN 6 52 ASN ** L 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN M 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.186271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143020 restraints weight = 41377.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.146244 restraints weight = 21406.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148399 restraints weight = 14600.937| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 23139 Z= 0.139 Angle : 0.708 47.580 32182 Z= 0.328 Chirality : 0.039 0.208 3297 Planarity : 0.004 0.052 3861 Dihedral : 8.905 85.726 3057 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.24 % Allowed : 2.78 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.17), residues: 2405 helix: 2.06 (0.13), residues: 1541 sheet: -1.43 (1.03), residues: 20 loop : -0.86 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 262 HIS 0.011 0.001 HIS X 21 PHE 0.034 0.002 PHE L 179 TYR 0.021 0.001 TYR 8 24 ARG 0.005 0.001 ARG 1 15 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 1286) hydrogen bonds : angle 4.10939 ( 3765) covalent geometry : bond 0.00309 (23119) covalent geometry : angle 0.70837 (32182) Misc. bond : bond 0.00150 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 799 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6734 (ptp90) cc_final: 0.6309 (mtm180) REVERT: A 40 SER cc_start: 0.7606 (p) cc_final: 0.7130 (t) REVERT: A 52 ASN cc_start: 0.6814 (m-40) cc_final: 0.5663 (t0) REVERT: B 21 HIS cc_start: 0.8390 (t-90) cc_final: 0.8108 (t-90) REVERT: D 34 ILE cc_start: 0.8262 (tp) cc_final: 0.7987 (tp) REVERT: D 51 TYR cc_start: 0.7077 (m-10) cc_final: 0.6823 (m-10) REVERT: F 15 ARG cc_start: 0.6588 (mmt90) cc_final: 0.6050 (ttm-80) REVERT: G 29 TRP cc_start: 0.8058 (m100) cc_final: 0.7805 (m100) REVERT: I 3 LYS cc_start: 0.7676 (mmtp) cc_final: 0.6401 (tptp) REVERT: I 43 TRP cc_start: 0.8349 (p90) cc_final: 0.8107 (p90) REVERT: J 13 THR cc_start: 0.7858 (p) cc_final: 0.7641 (t) REVERT: J 21 HIS cc_start: 0.8660 (t70) cc_final: 0.7824 (t70) REVERT: J 29 TRP cc_start: 0.8036 (m100) cc_final: 0.7568 (m-10) REVERT: K 1 MET cc_start: 0.3463 (mmm) cc_final: 0.2655 (tpt) REVERT: N 25 MET cc_start: 0.8651 (mmm) cc_final: 0.8336 (mmm) REVERT: P 19 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: Q 1 MET cc_start: 0.3051 (ptt) cc_final: 0.2807 (ttp) REVERT: Q 7 ILE cc_start: 0.7363 (mm) cc_final: 0.7072 (mm) REVERT: Q 23 PHE cc_start: 0.8449 (t80) cc_final: 0.8192 (t80) REVERT: Q 35 LEU cc_start: 0.9197 (mp) cc_final: 0.8789 (mp) REVERT: R 12 LEU cc_start: 0.8685 (mp) cc_final: 0.8158 (mp) REVERT: S 13 PRO cc_start: 0.8215 (Cg_endo) cc_final: 0.7808 (Cg_exo) REVERT: S 34 ILE cc_start: 0.8940 (mt) cc_final: 0.8629 (mm) REVERT: T 15 GLU cc_start: 0.8046 (pt0) cc_final: 0.7754 (tp30) REVERT: U 6 LYS cc_start: 0.7501 (mttp) cc_final: 0.6992 (mmtm) REVERT: U 12 ASP cc_start: 0.7182 (t70) cc_final: 0.6421 (t70) REVERT: W 5 TYR cc_start: 0.7760 (p90) cc_final: 0.7392 (p90) REVERT: W 6 LYS cc_start: 0.6628 (mttt) cc_final: 0.6359 (mptt) REVERT: W 15 ARG cc_start: 0.7115 (mpt90) cc_final: 0.5799 (ptm160) REVERT: W 27 LEU cc_start: 0.9255 (tp) cc_final: 0.8897 (tp) REVERT: W 43 TRP cc_start: 0.8390 (p90) cc_final: 0.7888 (p90) REVERT: X 14 ASP cc_start: 0.8084 (m-30) cc_final: 0.7833 (m-30) REVERT: X 42 VAL cc_start: 0.8584 (t) cc_final: 0.8310 (p) REVERT: Y 45 GLU cc_start: 0.8493 (tp30) cc_final: 0.8166 (tp30) REVERT: 1 11 PHE cc_start: 0.7582 (t80) cc_final: 0.7059 (t80) REVERT: 1 20 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: 1 23 PHE cc_start: 0.8830 (t80) cc_final: 0.8619 (t80) REVERT: 1 27 LEU cc_start: 0.9164 (tp) cc_final: 0.8951 (tp) REVERT: 1 37 SER cc_start: 0.8419 (p) cc_final: 0.8214 (p) REVERT: 2 13 THR cc_start: 0.7584 (p) cc_final: 0.7239 (t) REVERT: 2 14 ASP cc_start: 0.6809 (m-30) cc_final: 0.6461 (m-30) REVERT: 2 32 SER cc_start: 0.8679 (m) cc_final: 0.8418 (m) REVERT: 7 15 ARG cc_start: 0.7748 (mtt-85) cc_final: 0.7510 (tpp-160) REVERT: 7 36 LEU cc_start: 0.7927 (tt) cc_final: 0.7568 (tt) REVERT: 7 42 ASN cc_start: 0.7506 (t0) cc_final: 0.6954 (t0) REVERT: 8 15 GLU cc_start: 0.7299 (tp30) cc_final: 0.6823 (tp30) REVERT: 8 18 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7307 (tm-30) REVERT: 8 25 MET cc_start: 0.8230 (mmm) cc_final: 0.7638 (mmt) REVERT: 8 29 TRP cc_start: 0.7591 (m100) cc_final: 0.7055 (m100) REVERT: 9 5 TYR cc_start: 0.7120 (p90) cc_final: 0.6842 (p90) REVERT: 4 34 ILE cc_start: 0.8860 (mt) cc_final: 0.8344 (tp) REVERT: t 15 GLU cc_start: 0.7587 (mp0) cc_final: 0.7214 (mt-10) REVERT: t 18 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7151 (mt0) REVERT: t 29 TRP cc_start: 0.7280 (m100) cc_final: 0.6883 (m100) REVERT: t 46 ARG cc_start: 0.6621 (ttm170) cc_final: 0.5933 (tpt-90) REVERT: 6 5 TYR cc_start: 0.6153 (p90) cc_final: 0.5337 (p90) REVERT: C 43 TRP cc_start: 0.8681 (p90) cc_final: 0.8263 (p90) REVERT: L 59 TRP cc_start: 0.2519 (m100) cc_final: 0.2223 (p-90) REVERT: L 217 ARG cc_start: 0.4656 (mtp180) cc_final: 0.4446 (mtp180) REVERT: M 18 LEU cc_start: 0.5345 (mt) cc_final: 0.5006 (mt) REVERT: M 236 GLU cc_start: 0.4839 (mp0) cc_final: 0.4411 (pt0) REVERT: M 256 MET cc_start: 0.6063 (mmp) cc_final: 0.5811 (mmp) outliers start: 5 outliers final: 0 residues processed: 799 average time/residue: 0.3380 time to fit residues: 432.9513 Evaluate side-chains 721 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 719 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 83 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 222 optimal weight: 40.0000 chunk 218 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 195 optimal weight: 0.1980 chunk 201 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 52 ASN ** 3 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.185300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141945 restraints weight = 41860.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144888 restraints weight = 21656.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.146607 restraints weight = 14747.575| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23139 Z= 0.150 Angle : 0.716 47.529 32182 Z= 0.330 Chirality : 0.039 0.161 3297 Planarity : 0.004 0.051 3861 Dihedral : 8.792 85.523 3057 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.14 % Allowed : 2.54 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.17), residues: 2405 helix: 1.98 (0.13), residues: 1545 sheet: -1.36 (1.02), residues: 20 loop : -0.88 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 262 HIS 0.006 0.001 HIS 2 21 PHE 0.028 0.002 PHE L 179 TYR 0.020 0.001 TYR O 5 ARG 0.004 0.001 ARG Q 15 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 1286) hydrogen bonds : angle 4.03609 ( 3765) covalent geometry : bond 0.00341 (23119) covalent geometry : angle 0.71623 (32182) Misc. bond : bond 0.00138 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 781 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6723 (ptp90) cc_final: 0.6221 (mtm180) REVERT: A 40 SER cc_start: 0.7612 (p) cc_final: 0.7107 (t) REVERT: A 51 TYR cc_start: 0.6372 (m-10) cc_final: 0.6106 (m-10) REVERT: A 52 ASN cc_start: 0.6970 (m-40) cc_final: 0.5807 (t0) REVERT: B 21 HIS cc_start: 0.8357 (t-90) cc_final: 0.8001 (t70) REVERT: D 34 ILE cc_start: 0.8379 (tp) cc_final: 0.8160 (tp) REVERT: D 51 TYR cc_start: 0.7032 (m-10) cc_final: 0.6763 (m-10) REVERT: F 15 ARG cc_start: 0.6584 (mmt90) cc_final: 0.6077 (ttm-80) REVERT: F 42 ASN cc_start: 0.6850 (t0) cc_final: 0.6134 (t0) REVERT: G 29 TRP cc_start: 0.8093 (m100) cc_final: 0.7801 (m100) REVERT: G 43 TYR cc_start: 0.8282 (t80) cc_final: 0.7907 (t80) REVERT: J 21 HIS cc_start: 0.8621 (t70) cc_final: 0.7969 (t70) REVERT: J 29 TRP cc_start: 0.8069 (m100) cc_final: 0.7547 (m-10) REVERT: K 1 MET cc_start: 0.3749 (mmm) cc_final: 0.2794 (tpt) REVERT: N 25 MET cc_start: 0.8807 (mmm) cc_final: 0.8448 (mmm) REVERT: Q 1 MET cc_start: 0.3106 (ptt) cc_final: 0.2811 (ttp) REVERT: Q 7 ILE cc_start: 0.7400 (mm) cc_final: 0.7075 (mm) REVERT: Q 35 LEU cc_start: 0.9172 (mp) cc_final: 0.8950 (mp) REVERT: Q 51 TYR cc_start: 0.8423 (m-80) cc_final: 0.8132 (m-10) REVERT: R 12 LEU cc_start: 0.8709 (mp) cc_final: 0.8090 (mp) REVERT: S 17 PHE cc_start: 0.8194 (m-80) cc_final: 0.7906 (m-80) REVERT: S 34 ILE cc_start: 0.8953 (mt) cc_final: 0.8652 (mm) REVERT: T 15 GLU cc_start: 0.8013 (pt0) cc_final: 0.7758 (tp30) REVERT: T 25 MET cc_start: 0.8408 (mmm) cc_final: 0.8192 (mmm) REVERT: U 6 LYS cc_start: 0.7511 (mttp) cc_final: 0.7085 (mmmt) REVERT: V 9 TYR cc_start: 0.5281 (m-80) cc_final: 0.4440 (m-80) REVERT: W 15 ARG cc_start: 0.7117 (mpt90) cc_final: 0.5838 (ptt90) REVERT: X 14 ASP cc_start: 0.8089 (m-30) cc_final: 0.7826 (m-30) REVERT: X 42 VAL cc_start: 0.8524 (t) cc_final: 0.8183 (p) REVERT: Y 14 ARG cc_start: 0.7444 (mtp180) cc_final: 0.7242 (mtp85) REVERT: Y 25 PHE cc_start: 0.8712 (t80) cc_final: 0.8458 (t80) REVERT: Y 45 GLU cc_start: 0.8494 (tp30) cc_final: 0.8214 (tp30) REVERT: 1 27 LEU cc_start: 0.9163 (tp) cc_final: 0.8942 (tp) REVERT: 2 13 THR cc_start: 0.7531 (p) cc_final: 0.7178 (t) REVERT: 2 14 ASP cc_start: 0.6814 (m-30) cc_final: 0.6389 (m-30) REVERT: 2 32 SER cc_start: 0.8723 (m) cc_final: 0.8505 (m) REVERT: 7 9 MET cc_start: 0.6041 (mtm) cc_final: 0.4490 (mtt) REVERT: 7 14 ARG cc_start: 0.7726 (mtp180) cc_final: 0.7016 (mpp80) REVERT: 7 36 LEU cc_start: 0.7901 (tt) cc_final: 0.7533 (tt) REVERT: 7 42 ASN cc_start: 0.7482 (t0) cc_final: 0.6943 (t0) REVERT: 8 15 GLU cc_start: 0.7222 (tp30) cc_final: 0.6748 (tp30) REVERT: 8 18 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7431 (tm-30) REVERT: 8 25 MET cc_start: 0.8200 (mmm) cc_final: 0.7395 (mmt) REVERT: 8 29 TRP cc_start: 0.7776 (m100) cc_final: 0.7208 (m100) REVERT: 4 34 ILE cc_start: 0.8921 (mt) cc_final: 0.8425 (tp) REVERT: t 15 GLU cc_start: 0.7682 (mp0) cc_final: 0.7288 (mt-10) REVERT: t 18 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7151 (mt0) REVERT: t 29 TRP cc_start: 0.7243 (m100) cc_final: 0.6818 (m100) REVERT: 6 5 TYR cc_start: 0.6083 (p90) cc_final: 0.5226 (p90) REVERT: 6 17 PHE cc_start: 0.8810 (m-80) cc_final: 0.8609 (m-80) REVERT: 5 25 MET cc_start: 0.8480 (mmp) cc_final: 0.8104 (mmp) REVERT: C 6 LYS cc_start: 0.7787 (mppt) cc_final: 0.6359 (mmmt) REVERT: C 43 TRP cc_start: 0.8677 (p90) cc_final: 0.8256 (p90) REVERT: M 184 ASP cc_start: 0.5729 (t0) cc_final: 0.5275 (m-30) REVERT: M 236 GLU cc_start: 0.4901 (mp0) cc_final: 0.4476 (pt0) REVERT: M 256 MET cc_start: 0.6084 (mmp) cc_final: 0.5726 (mmp) REVERT: M 272 MET cc_start: 0.2242 (ttm) cc_final: 0.2009 (tpp) outliers start: 3 outliers final: 0 residues processed: 781 average time/residue: 0.3145 time to fit residues: 393.3983 Evaluate side-chains 707 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 707 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 23 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 225 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 165 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 52 ASN ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.186472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142443 restraints weight = 41522.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145729 restraints weight = 21135.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.147678 restraints weight = 14175.743| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 23139 Z= 0.123 Angle : 0.686 47.777 32182 Z= 0.314 Chirality : 0.037 0.152 3297 Planarity : 0.004 0.051 3861 Dihedral : 8.616 89.520 3057 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.14 % Allowed : 2.49 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.17), residues: 2405 helix: 2.09 (0.13), residues: 1548 sheet: -1.37 (1.05), residues: 20 loop : -0.87 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP W 43 HIS 0.004 0.001 HIS 8 21 PHE 0.048 0.001 PHE 1 11 TYR 0.024 0.001 TYR O 5 ARG 0.005 0.000 ARG W 53 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 1286) hydrogen bonds : angle 3.92084 ( 3765) covalent geometry : bond 0.00277 (23119) covalent geometry : angle 0.68619 (32182) Misc. bond : bond 0.00103 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 782 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6621 (ptp90) cc_final: 0.6094 (mtm180) REVERT: A 40 SER cc_start: 0.7619 (p) cc_final: 0.7150 (t) REVERT: A 41 TYR cc_start: 0.5600 (t80) cc_final: 0.5297 (t80) REVERT: A 52 ASN cc_start: 0.6988 (m-40) cc_final: 0.5896 (t0) REVERT: B 14 ASP cc_start: 0.6160 (p0) cc_final: 0.5909 (t0) REVERT: B 21 HIS cc_start: 0.8328 (t-90) cc_final: 0.8122 (t-90) REVERT: D 34 ILE cc_start: 0.8380 (tp) cc_final: 0.8179 (tp) REVERT: D 51 TYR cc_start: 0.7090 (m-10) cc_final: 0.6790 (m-10) REVERT: E 25 MET cc_start: 0.7056 (mmm) cc_final: 0.6812 (mmm) REVERT: F 15 ARG cc_start: 0.6557 (mmt90) cc_final: 0.6034 (ttm-80) REVERT: F 42 ASN cc_start: 0.6783 (t0) cc_final: 0.6086 (t0) REVERT: G 29 TRP cc_start: 0.8105 (m100) cc_final: 0.7871 (m100) REVERT: G 43 TYR cc_start: 0.8269 (t80) cc_final: 0.8041 (t80) REVERT: I 3 LYS cc_start: 0.7611 (mmtp) cc_final: 0.6331 (tptp) REVERT: J 13 THR cc_start: 0.7487 (t) cc_final: 0.7226 (t) REVERT: J 16 GLN cc_start: 0.7311 (mt0) cc_final: 0.6609 (mp10) REVERT: J 21 HIS cc_start: 0.8592 (t70) cc_final: 0.7949 (t70) REVERT: J 29 TRP cc_start: 0.8099 (m100) cc_final: 0.7554 (m-10) REVERT: K 1 MET cc_start: 0.3717 (mmm) cc_final: 0.2730 (tpt) REVERT: K 52 ASN cc_start: 0.6936 (m110) cc_final: 0.6683 (t0) REVERT: N 25 MET cc_start: 0.8766 (mmm) cc_final: 0.8467 (mmm) REVERT: Q 1 MET cc_start: 0.3119 (ptt) cc_final: 0.2825 (ttp) REVERT: Q 7 ILE cc_start: 0.7394 (mm) cc_final: 0.7125 (mm) REVERT: Q 35 LEU cc_start: 0.9115 (mp) cc_final: 0.8893 (mp) REVERT: Q 51 TYR cc_start: 0.8454 (m-80) cc_final: 0.8168 (m-10) REVERT: R 10 THR cc_start: 0.7139 (p) cc_final: 0.6573 (t) REVERT: R 12 LEU cc_start: 0.8705 (mp) cc_final: 0.8095 (mp) REVERT: S 13 PRO cc_start: 0.8160 (Cg_endo) cc_final: 0.7880 (Cg_exo) REVERT: S 17 PHE cc_start: 0.8149 (m-80) cc_final: 0.7816 (m-80) REVERT: S 34 ILE cc_start: 0.8947 (mt) cc_final: 0.8648 (mm) REVERT: T 15 GLU cc_start: 0.8055 (pt0) cc_final: 0.7760 (tp30) REVERT: T 25 MET cc_start: 0.8444 (mmm) cc_final: 0.8241 (mmm) REVERT: U 6 LYS cc_start: 0.7326 (mttp) cc_final: 0.6972 (mmmt) REVERT: U 9 MET cc_start: 0.7608 (ppp) cc_final: 0.7239 (ppp) REVERT: U 12 ASP cc_start: 0.7762 (t0) cc_final: 0.7038 (t70) REVERT: V 9 TYR cc_start: 0.4749 (m-80) cc_final: 0.4376 (m-80) REVERT: W 15 ARG cc_start: 0.7075 (mpt90) cc_final: 0.5734 (ptm-80) REVERT: W 27 LEU cc_start: 0.9159 (tp) cc_final: 0.8938 (tp) REVERT: X 14 ASP cc_start: 0.7866 (m-30) cc_final: 0.7578 (m-30) REVERT: X 42 VAL cc_start: 0.8443 (t) cc_final: 0.8122 (p) REVERT: Y 25 PHE cc_start: 0.8706 (t80) cc_final: 0.8479 (t80) REVERT: Z 15 GLU cc_start: 0.7049 (pp20) cc_final: 0.6706 (pp20) REVERT: 1 27 LEU cc_start: 0.9126 (tp) cc_final: 0.8920 (tp) REVERT: 1 37 SER cc_start: 0.8450 (p) cc_final: 0.8221 (p) REVERT: 2 13 THR cc_start: 0.7542 (p) cc_final: 0.7233 (t) REVERT: 2 14 ASP cc_start: 0.6853 (m-30) cc_final: 0.6479 (m-30) REVERT: 2 32 SER cc_start: 0.8678 (m) cc_final: 0.8477 (m) REVERT: 7 9 MET cc_start: 0.6014 (mtm) cc_final: 0.4499 (mtt) REVERT: 7 14 ARG cc_start: 0.7693 (mtp180) cc_final: 0.7013 (mpp80) REVERT: 7 24 LEU cc_start: 0.7671 (mt) cc_final: 0.7435 (mt) REVERT: 7 42 ASN cc_start: 0.7494 (t0) cc_final: 0.6995 (t0) REVERT: 8 15 GLU cc_start: 0.7220 (tp30) cc_final: 0.6765 (tp30) REVERT: 8 18 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7419 (tm-30) REVERT: 8 25 MET cc_start: 0.8062 (mmm) cc_final: 0.7505 (mmt) REVERT: 8 29 TRP cc_start: 0.7831 (m100) cc_final: 0.7208 (m100) REVERT: 4 34 ILE cc_start: 0.8902 (mt) cc_final: 0.8385 (tp) REVERT: t 15 GLU cc_start: 0.7670 (mp0) cc_final: 0.7307 (mt-10) REVERT: t 18 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7156 (mt0) REVERT: t 29 TRP cc_start: 0.7287 (m100) cc_final: 0.6846 (m100) REVERT: 6 5 TYR cc_start: 0.6127 (p90) cc_final: 0.5211 (p90) REVERT: 5 25 MET cc_start: 0.8458 (mmp) cc_final: 0.8242 (mmm) REVERT: C 6 LYS cc_start: 0.7638 (mppt) cc_final: 0.6366 (mmmt) REVERT: C 43 TRP cc_start: 0.8665 (p90) cc_final: 0.8292 (p90) REVERT: M 184 ASP cc_start: 0.5711 (t0) cc_final: 0.5296 (m-30) REVERT: M 236 GLU cc_start: 0.4671 (mp0) cc_final: 0.4254 (pt0) REVERT: M 256 MET cc_start: 0.5953 (mmp) cc_final: 0.5571 (mmp) REVERT: M 272 MET cc_start: 0.2129 (ttm) cc_final: 0.1888 (tpp) outliers start: 3 outliers final: 0 residues processed: 782 average time/residue: 0.3189 time to fit residues: 399.7575 Evaluate side-chains 707 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 707 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 96 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 183 optimal weight: 0.0770 chunk 178 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 229 optimal weight: 0.0370 chunk 80 optimal weight: 9.9990 overall best weight: 2.4220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 GLN 2 21 HIS ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 16 GLN M 182 HIS ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.185546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.150919 restraints weight = 41423.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155762 restraints weight = 41388.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154981 restraints weight = 20944.111| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 23139 Z= 0.150 Angle : 0.716 47.542 32182 Z= 0.328 Chirality : 0.039 0.155 3297 Planarity : 0.004 0.060 3861 Dihedral : 8.618 86.207 3057 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.05 % Allowed : 2.16 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.17), residues: 2405 helix: 2.02 (0.13), residues: 1550 sheet: 1.01 (1.47), residues: 10 loop : -0.92 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP W 43 HIS 0.005 0.001 HIS 8 21 PHE 0.025 0.002 PHE U 17 TYR 0.020 0.001 TYR O 5 ARG 0.007 0.001 ARG Q 15 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 1286) hydrogen bonds : angle 3.93290 ( 3765) covalent geometry : bond 0.00348 (23119) covalent geometry : angle 0.71583 (32182) Misc. bond : bond 0.00151 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 771 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6642 (ptp90) cc_final: 0.6191 (mtm180) REVERT: A 40 SER cc_start: 0.7649 (p) cc_final: 0.7145 (t) REVERT: A 41 TYR cc_start: 0.5719 (t80) cc_final: 0.5406 (t80) REVERT: A 51 TYR cc_start: 0.6274 (m-10) cc_final: 0.6025 (m-10) REVERT: A 52 ASN cc_start: 0.6851 (m-40) cc_final: 0.5793 (t0) REVERT: D 51 TYR cc_start: 0.7036 (m-10) cc_final: 0.6777 (m-10) REVERT: F 15 ARG cc_start: 0.6693 (mmt90) cc_final: 0.6175 (ttm-80) REVERT: F 20 GLN cc_start: 0.6829 (tm-30) cc_final: 0.6276 (tm-30) REVERT: F 42 ASN cc_start: 0.6835 (t0) cc_final: 0.6155 (t0) REVERT: G 29 TRP cc_start: 0.7912 (m100) cc_final: 0.7694 (m100) REVERT: G 43 TYR cc_start: 0.8233 (t80) cc_final: 0.7959 (t80) REVERT: J 13 THR cc_start: 0.7522 (t) cc_final: 0.7241 (t) REVERT: J 16 GLN cc_start: 0.7338 (mt0) cc_final: 0.6468 (mp10) REVERT: J 21 HIS cc_start: 0.8520 (t70) cc_final: 0.7828 (t70) REVERT: J 29 TRP cc_start: 0.8012 (m100) cc_final: 0.7491 (m-10) REVERT: K 1 MET cc_start: 0.3777 (mmm) cc_final: 0.3374 (mmm) REVERT: N 10 THR cc_start: 0.9008 (p) cc_final: 0.8586 (p) REVERT: N 25 MET cc_start: 0.8827 (mmm) cc_final: 0.8520 (mmm) REVERT: Q 1 MET cc_start: 0.3122 (ptt) cc_final: 0.2753 (ttp) REVERT: Q 7 ILE cc_start: 0.7263 (mm) cc_final: 0.7015 (mm) REVERT: Q 35 LEU cc_start: 0.9051 (mp) cc_final: 0.8849 (mp) REVERT: Q 51 TYR cc_start: 0.8435 (m-80) cc_final: 0.8214 (m-10) REVERT: R 10 THR cc_start: 0.7321 (p) cc_final: 0.6682 (t) REVERT: R 12 LEU cc_start: 0.8675 (mp) cc_final: 0.8032 (mp) REVERT: S 34 ILE cc_start: 0.8978 (mt) cc_final: 0.8710 (mm) REVERT: T 15 GLU cc_start: 0.7879 (pt0) cc_final: 0.7632 (tp30) REVERT: U 6 LYS cc_start: 0.7317 (mttp) cc_final: 0.6980 (mmmt) REVERT: U 15 ARG cc_start: 0.6672 (ptt180) cc_final: 0.5007 (ptm-80) REVERT: W 15 ARG cc_start: 0.7084 (mpt90) cc_final: 0.5709 (ptm-80) REVERT: W 41 TYR cc_start: 0.8087 (m-80) cc_final: 0.7825 (m-80) REVERT: X 14 ASP cc_start: 0.7841 (m-30) cc_final: 0.7597 (m-30) REVERT: X 42 VAL cc_start: 0.8432 (t) cc_final: 0.8206 (p) REVERT: Y 45 GLU cc_start: 0.8437 (tp30) cc_final: 0.8205 (tp30) REVERT: Z 15 GLU cc_start: 0.6907 (pp20) cc_final: 0.6650 (pp20) REVERT: 1 9 MET cc_start: 0.6004 (ptp) cc_final: 0.4667 (ttt) REVERT: 1 11 PHE cc_start: 0.7289 (t80) cc_final: 0.7027 (t80) REVERT: 1 17 PHE cc_start: 0.8326 (m-80) cc_final: 0.8079 (m-80) REVERT: 1 37 SER cc_start: 0.8454 (p) cc_final: 0.8222 (p) REVERT: 2 13 THR cc_start: 0.7429 (p) cc_final: 0.7159 (t) REVERT: 2 14 ASP cc_start: 0.6844 (m-30) cc_final: 0.6308 (m-30) REVERT: 2 21 HIS cc_start: 0.8024 (t-170) cc_final: 0.7196 (t-170) REVERT: 2 32 SER cc_start: 0.8727 (m) cc_final: 0.8524 (m) REVERT: 7 9 MET cc_start: 0.5975 (mtm) cc_final: 0.4461 (mtt) REVERT: 7 14 ARG cc_start: 0.7647 (mtp180) cc_final: 0.6982 (mpp80) REVERT: 7 36 LEU cc_start: 0.7915 (tt) cc_final: 0.7614 (tt) REVERT: 7 42 ASN cc_start: 0.7441 (t0) cc_final: 0.6914 (t0) REVERT: 8 15 GLU cc_start: 0.7163 (tp30) cc_final: 0.6714 (tp30) REVERT: 8 18 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7408 (tm-30) REVERT: 0 21 HIS cc_start: 0.8598 (t70) cc_final: 0.8089 (t70) REVERT: 4 34 ILE cc_start: 0.8889 (mt) cc_final: 0.8368 (tp) REVERT: t 15 GLU cc_start: 0.7507 (mp0) cc_final: 0.7207 (mt-10) REVERT: t 18 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7166 (mt0) REVERT: t 29 TRP cc_start: 0.7191 (m100) cc_final: 0.6774 (m100) REVERT: 6 5 TYR cc_start: 0.6073 (p90) cc_final: 0.5227 (p90) REVERT: 6 17 PHE cc_start: 0.8534 (m-80) cc_final: 0.8200 (m-80) REVERT: 5 43 TYR cc_start: 0.7144 (t80) cc_final: 0.6565 (t80) REVERT: C 6 LYS cc_start: 0.7674 (mppt) cc_final: 0.6439 (mmmt) REVERT: C 43 TRP cc_start: 0.8573 (p90) cc_final: 0.8149 (p90) REVERT: 3 19 GLU cc_start: 0.7751 (tp30) cc_final: 0.7519 (tp30) REVERT: L 115 TYR cc_start: 0.1997 (m-10) cc_final: 0.1203 (m-80) REVERT: M 75 TRP cc_start: 0.4568 (m100) cc_final: 0.4360 (m100) REVERT: M 142 MET cc_start: 0.4711 (mmm) cc_final: 0.4168 (mmt) REVERT: M 182 HIS cc_start: 0.5616 (t70) cc_final: 0.4969 (t-90) REVERT: M 184 ASP cc_start: 0.5828 (t0) cc_final: 0.5514 (m-30) REVERT: M 272 MET cc_start: 0.3004 (ttm) cc_final: 0.2700 (tpp) outliers start: 1 outliers final: 1 residues processed: 771 average time/residue: 0.2997 time to fit residues: 370.6962 Evaluate side-chains 706 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 705 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 25 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 210 optimal weight: 30.0000 chunk 141 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN 0 21 HIS ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 16 GLN ** L 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 HIS ** 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 = 0.4203 r_free = 0.4203 target = 0.182795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.147598 restraints weight = 42144.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150224 restraints weight = 41689.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.149955 restraints weight = 26212.489| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23139 Z= 0.210 Angle : 0.782 47.463 32182 Z= 0.363 Chirality : 0.041 0.170 3297 Planarity : 0.005 0.050 3861 Dihedral : 8.950 84.759 3057 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.17), residues: 2405 helix: 1.77 (0.13), residues: 1547 sheet: 1.03 (1.42), residues: 10 loop : -1.06 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 73 HIS 0.012 0.001 HIS B 21 PHE 0.039 0.002 PHE 1 11 TYR 0.021 0.002 TYR 9 5 ARG 0.008 0.001 ARG Q 15 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 1286) hydrogen bonds : angle 4.12654 ( 3765) covalent geometry : bond 0.00489 (23119) covalent geometry : angle 0.78246 (32182) Misc. bond : bond 0.00218 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 745 time to evaluate : 2.261 Fit side-chains revert: symmetry clash REVERT: A 40 SER cc_start: 0.7575 (p) cc_final: 0.7076 (t) REVERT: D 34 ILE cc_start: 0.8316 (tp) cc_final: 0.8112 (tp) REVERT: D 51 TYR cc_start: 0.7064 (m-10) cc_final: 0.6864 (m-10) REVERT: F 15 ARG cc_start: 0.6848 (mmt90) cc_final: 0.6352 (ttm-80) REVERT: F 20 GLN cc_start: 0.6591 (tm-30) cc_final: 0.6099 (tm-30) REVERT: F 42 ASN cc_start: 0.6830 (t0) cc_final: 0.6172 (t0) REVERT: G 43 TYR cc_start: 0.8245 (t80) cc_final: 0.7950 (t80) REVERT: I 3 LYS cc_start: 0.7706 (mmtp) cc_final: 0.6405 (tptp) REVERT: J 14 ASP cc_start: 0.7576 (m-30) cc_final: 0.7371 (m-30) REVERT: J 16 GLN cc_start: 0.7430 (mt0) cc_final: 0.6709 (mp10) REVERT: J 21 HIS cc_start: 0.8440 (t70) cc_final: 0.7766 (t70) REVERT: J 29 TRP cc_start: 0.8005 (m100) cc_final: 0.7497 (m-10) REVERT: K 1 MET cc_start: 0.3733 (mmm) cc_final: 0.3344 (mmm) REVERT: N 10 THR cc_start: 0.9081 (p) cc_final: 0.8817 (m) REVERT: Q 1 MET cc_start: 0.3127 (ptt) cc_final: 0.2863 (ptt) REVERT: Q 7 ILE cc_start: 0.7239 (mm) cc_final: 0.7025 (mm) REVERT: Q 35 LEU cc_start: 0.9148 (mp) cc_final: 0.8924 (mp) REVERT: R 10 THR cc_start: 0.7373 (p) cc_final: 0.6816 (t) REVERT: R 12 LEU cc_start: 0.8624 (mp) cc_final: 0.8034 (mp) REVERT: S 34 ILE cc_start: 0.9007 (mt) cc_final: 0.8712 (mm) REVERT: U 6 LYS cc_start: 0.7579 (mttp) cc_final: 0.7036 (mmtm) REVERT: U 15 ARG cc_start: 0.6723 (ptt180) cc_final: 0.4985 (ptm-80) REVERT: V 21 HIS cc_start: 0.8246 (t70) cc_final: 0.7992 (t-170) REVERT: W 5 TYR cc_start: 0.7854 (p90) cc_final: 0.7614 (p90) REVERT: W 15 ARG cc_start: 0.7111 (mpt90) cc_final: 0.5749 (ptm-80) REVERT: W 30 MET cc_start: 0.7641 (ttm) cc_final: 0.7401 (ttm) REVERT: X 14 ASP cc_start: 0.7954 (m-30) cc_final: 0.7748 (m-30) REVERT: X 42 VAL cc_start: 0.8422 (t) cc_final: 0.8222 (p) REVERT: Y 25 PHE cc_start: 0.8696 (t80) cc_final: 0.8438 (t80) REVERT: Y 45 GLU cc_start: 0.8522 (tp30) cc_final: 0.8287 (tp30) REVERT: Z 15 GLU cc_start: 0.6858 (pp20) cc_final: 0.6574 (pp20) REVERT: 1 9 MET cc_start: 0.5819 (ptp) cc_final: 0.4792 (tmm) REVERT: 1 17 PHE cc_start: 0.8327 (m-80) cc_final: 0.8093 (m-80) REVERT: 1 37 SER cc_start: 0.8479 (p) cc_final: 0.8238 (p) REVERT: 2 14 ASP cc_start: 0.6786 (m-30) cc_final: 0.6345 (m-30) REVERT: 2 32 SER cc_start: 0.8777 (m) cc_final: 0.8498 (m) REVERT: 7 9 MET cc_start: 0.6124 (mtm) cc_final: 0.4514 (mtt) REVERT: 7 14 ARG cc_start: 0.7636 (mtp180) cc_final: 0.6996 (mpp80) REVERT: 7 36 LEU cc_start: 0.7906 (tt) cc_final: 0.7560 (tt) REVERT: 7 42 ASN cc_start: 0.7456 (t0) cc_final: 0.6999 (t0) REVERT: 8 15 GLU cc_start: 0.7248 (tp30) cc_final: 0.6717 (tp30) REVERT: 8 18 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7455 (tm-30) REVERT: 4 34 ILE cc_start: 0.8917 (mt) cc_final: 0.8372 (tp) REVERT: t 15 GLU cc_start: 0.7461 (mp0) cc_final: 0.7173 (mt-10) REVERT: t 18 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7616 (mt0) REVERT: t 29 TRP cc_start: 0.7381 (m100) cc_final: 0.6878 (m100) REVERT: 6 5 TYR cc_start: 0.6253 (p90) cc_final: 0.5309 (p90) REVERT: 5 43 TYR cc_start: 0.7364 (t80) cc_final: 0.6498 (t80) REVERT: C 6 LYS cc_start: 0.7780 (mppt) cc_final: 0.6470 (mmmt) REVERT: C 43 TRP cc_start: 0.8572 (p90) cc_final: 0.8142 (p90) REVERT: L 167 PHE cc_start: 0.6121 (t80) cc_final: 0.5699 (t80) REVERT: M 182 HIS cc_start: 0.6232 (t70) cc_final: 0.5455 (t-90) REVERT: M 184 ASP cc_start: 0.5754 (t0) cc_final: 0.5281 (m-30) REVERT: M 272 MET cc_start: 0.3182 (ttm) cc_final: 0.2888 (tpp) outliers start: 1 outliers final: 0 residues processed: 746 average time/residue: 0.2936 time to fit residues: 351.5248 Evaluate side-chains 688 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 103 optimal weight: 0.8980 chunk 191 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 16 GLN ** L 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.185875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150235 restraints weight = 41701.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153072 restraints weight = 39501.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.152669 restraints weight = 24831.137| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 23139 Z= 0.135 Angle : 0.718 47.795 32182 Z= 0.332 Chirality : 0.039 0.156 3297 Planarity : 0.004 0.051 3861 Dihedral : 8.745 89.240 3057 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.17), residues: 2405 helix: 1.90 (0.13), residues: 1547 sheet: 1.01 (1.34), residues: 10 loop : -1.07 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP J 45 HIS 0.013 0.001 HIS B 21 PHE 0.035 0.002 PHE S 17 TYR 0.019 0.001 TYR O 5 ARG 0.010 0.001 ARG Q 15 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 1286) hydrogen bonds : angle 3.99715 ( 3765) covalent geometry : bond 0.00307 (23119) covalent geometry : angle 0.71768 (32182) Misc. bond : bond 0.00111 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 766 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6993 (ptp90) cc_final: 0.6281 (mtm180) REVERT: A 40 SER cc_start: 0.7663 (p) cc_final: 0.7157 (t) REVERT: A 51 TYR cc_start: 0.6130 (m-10) cc_final: 0.5908 (m-10) REVERT: A 52 ASN cc_start: 0.6810 (m-40) cc_final: 0.5850 (t0) REVERT: B 14 ASP cc_start: 0.5778 (t0) cc_final: 0.5425 (t0) REVERT: D 34 ILE cc_start: 0.8292 (tp) cc_final: 0.8065 (tp) REVERT: F 20 GLN cc_start: 0.6713 (tm-30) cc_final: 0.6339 (tm-30) REVERT: I 3 LYS cc_start: 0.7702 (mmtp) cc_final: 0.6404 (tptp) REVERT: I 43 TRP cc_start: 0.8271 (p90) cc_final: 0.8048 (p90) REVERT: J 16 GLN cc_start: 0.7168 (mt0) cc_final: 0.6443 (mp10) REVERT: J 21 HIS cc_start: 0.8364 (t70) cc_final: 0.8142 (t70) REVERT: J 29 TRP cc_start: 0.7997 (m100) cc_final: 0.7519 (m-10) REVERT: K 1 MET cc_start: 0.3797 (mmm) cc_final: 0.3429 (mmm) REVERT: N 10 THR cc_start: 0.9098 (p) cc_final: 0.8671 (p) REVERT: N 25 MET cc_start: 0.8596 (mmm) cc_final: 0.8310 (mmm) REVERT: Q 1 MET cc_start: 0.2975 (ptt) cc_final: 0.2617 (ptt) REVERT: Q 7 ILE cc_start: 0.7310 (mm) cc_final: 0.7048 (mm) REVERT: Q 51 TYR cc_start: 0.8412 (m-80) cc_final: 0.8178 (m-10) REVERT: R 10 THR cc_start: 0.7345 (p) cc_final: 0.6796 (t) REVERT: R 12 LEU cc_start: 0.8673 (mp) cc_final: 0.7955 (mp) REVERT: S 17 PHE cc_start: 0.8130 (m-80) cc_final: 0.6653 (t80) REVERT: S 34 ILE cc_start: 0.8978 (mt) cc_final: 0.8702 (mm) REVERT: U 6 LYS cc_start: 0.7370 (mttp) cc_final: 0.6921 (mmmt) REVERT: U 15 ARG cc_start: 0.6492 (ptt180) cc_final: 0.4900 (ptm-80) REVERT: W 15 ARG cc_start: 0.7220 (mpt90) cc_final: 0.5675 (mtm110) REVERT: W 30 MET cc_start: 0.7663 (ttm) cc_final: 0.7317 (ttm) REVERT: X 14 ASP cc_start: 0.7856 (m-30) cc_final: 0.7584 (m-30) REVERT: Y 14 ARG cc_start: 0.6903 (mtp180) cc_final: 0.6258 (mtp85) REVERT: Y 25 PHE cc_start: 0.8684 (t80) cc_final: 0.8406 (t80) REVERT: Z 15 GLU cc_start: 0.6974 (pp20) cc_final: 0.6718 (pp20) REVERT: 1 9 MET cc_start: 0.6052 (ptp) cc_final: 0.4877 (tmm) REVERT: 1 10 ILE cc_start: 0.3689 (tp) cc_final: 0.3485 (tp) REVERT: 1 17 PHE cc_start: 0.8424 (m-80) cc_final: 0.8070 (m-80) REVERT: 1 37 SER cc_start: 0.8370 (p) cc_final: 0.8091 (p) REVERT: 2 13 THR cc_start: 0.7150 (p) cc_final: 0.6775 (t) REVERT: 2 14 ASP cc_start: 0.6722 (m-30) cc_final: 0.6361 (m-30) REVERT: 7 9 MET cc_start: 0.5899 (mtm) cc_final: 0.4377 (mtt) REVERT: 7 14 ARG cc_start: 0.7608 (mtp180) cc_final: 0.6951 (mpp80) REVERT: 7 36 LEU cc_start: 0.8010 (tt) cc_final: 0.7671 (tt) REVERT: 7 42 ASN cc_start: 0.7461 (t0) cc_final: 0.6918 (t0) REVERT: 8 15 GLU cc_start: 0.7237 (tp30) cc_final: 0.6809 (tp30) REVERT: 8 18 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7528 (tm-30) REVERT: 4 34 ILE cc_start: 0.8893 (mt) cc_final: 0.8344 (tp) REVERT: t 15 GLU cc_start: 0.7559 (mp0) cc_final: 0.7293 (mt-10) REVERT: t 18 GLN cc_start: 0.7835 (tp-100) cc_final: 0.7600 (mt0) REVERT: t 24 TYR cc_start: 0.7788 (t80) cc_final: 0.7328 (t80) REVERT: t 29 TRP cc_start: 0.7327 (m100) cc_final: 0.6869 (m100) REVERT: 6 5 TYR cc_start: 0.6072 (p90) cc_final: 0.5129 (p90) REVERT: 5 43 TYR cc_start: 0.7342 (t80) cc_final: 0.6518 (t80) REVERT: C 6 LYS cc_start: 0.7680 (mppt) cc_final: 0.6459 (mmmt) REVERT: C 43 TRP cc_start: 0.8544 (p90) cc_final: 0.8183 (p90) REVERT: L 139 MET cc_start: 0.4420 (mpp) cc_final: 0.4102 (mpp) REVERT: L 167 PHE cc_start: 0.6042 (t80) cc_final: 0.5551 (t80) REVERT: M 184 ASP cc_start: 0.5714 (t0) cc_final: 0.5291 (m-30) REVERT: M 250 LEU cc_start: 0.4644 (mt) cc_final: 0.4420 (mt) REVERT: M 272 MET cc_start: 0.2993 (ttm) cc_final: 0.2694 (tpp) outliers start: 0 outliers final: 0 residues processed: 766 average time/residue: 0.2875 time to fit residues: 353.4341 Evaluate side-chains 695 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 124 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN 2 21 HIS ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 16 GLN ** M 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 HIS ** 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 = 0.4220 r_free = 0.4220 target = 0.184112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149057 restraints weight = 41735.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153428 restraints weight = 48906.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.152606 restraints weight = 24760.765| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 23139 Z= 0.176 Angle : 0.767 47.474 32182 Z= 0.354 Chirality : 0.041 0.189 3297 Planarity : 0.004 0.059 3861 Dihedral : 8.818 84.997 3057 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.05 % Allowed : 0.81 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.17), residues: 2405 helix: 1.81 (0.13), residues: 1546 sheet: 1.06 (1.41), residues: 10 loop : -1.11 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP J 45 HIS 0.012 0.001 HIS B 21 PHE 0.034 0.002 PHE 1 11 TYR 0.025 0.002 TYR 8 24 ARG 0.009 0.001 ARG M 228 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 1286) hydrogen bonds : angle 4.08932 ( 3765) covalent geometry : bond 0.00413 (23119) covalent geometry : angle 0.76670 (32182) Misc. bond : bond 0.00186 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 741 time to evaluate : 2.187 Fit side-chains REVERT: A 14 ARG cc_start: 0.6967 (ptp90) cc_final: 0.6265 (mtm180) REVERT: A 40 SER cc_start: 0.7566 (p) cc_final: 0.7124 (t) REVERT: A 51 TYR cc_start: 0.6206 (m-10) cc_final: 0.5949 (m-10) REVERT: A 52 ASN cc_start: 0.6833 (m-40) cc_final: 0.5853 (t0) REVERT: D 34 ILE cc_start: 0.8267 (tp) cc_final: 0.8066 (tp) REVERT: F 20 GLN cc_start: 0.6613 (tm-30) cc_final: 0.6213 (tm-30) REVERT: I 8 TRP cc_start: 0.8722 (m100) cc_final: 0.8497 (m100) REVERT: J 16 GLN cc_start: 0.7045 (mt0) cc_final: 0.6295 (mp10) REVERT: J 21 HIS cc_start: 0.8589 (t70) cc_final: 0.7730 (t70) REVERT: J 29 TRP cc_start: 0.8012 (m100) cc_final: 0.7562 (m-10) REVERT: K 1 MET cc_start: 0.3845 (mmm) cc_final: 0.3567 (mmm) REVERT: N 10 THR cc_start: 0.9052 (p) cc_final: 0.8195 (t) REVERT: N 25 MET cc_start: 0.8653 (mmm) cc_final: 0.8354 (mmm) REVERT: Q 1 MET cc_start: 0.3017 (ptt) cc_final: 0.2703 (ptt) REVERT: Q 7 ILE cc_start: 0.7272 (mm) cc_final: 0.7022 (mm) REVERT: Q 51 TYR cc_start: 0.8407 (m-80) cc_final: 0.8080 (m-10) REVERT: R 10 THR cc_start: 0.7561 (p) cc_final: 0.7004 (t) REVERT: R 12 LEU cc_start: 0.8746 (mp) cc_final: 0.8062 (mp) REVERT: S 17 PHE cc_start: 0.8140 (m-80) cc_final: 0.6716 (t80) REVERT: S 34 ILE cc_start: 0.9062 (mt) cc_final: 0.8767 (mm) REVERT: U 6 LYS cc_start: 0.7427 (mttp) cc_final: 0.6926 (mmtm) REVERT: U 15 ARG cc_start: 0.6563 (ptt180) cc_final: 0.4964 (ptm-80) REVERT: V 21 HIS cc_start: 0.8237 (t70) cc_final: 0.7988 (t-170) REVERT: W 5 TYR cc_start: 0.7876 (p90) cc_final: 0.7675 (p90) REVERT: W 15 ARG cc_start: 0.6835 (mpt90) cc_final: 0.5689 (mtm110) REVERT: W 30 MET cc_start: 0.7715 (ttm) cc_final: 0.7228 (ttm) REVERT: X 14 ASP cc_start: 0.7897 (m-30) cc_final: 0.7658 (m-30) REVERT: Y 14 ARG cc_start: 0.7034 (mtp180) cc_final: 0.6351 (mtp85) REVERT: Y 25 PHE cc_start: 0.8703 (t80) cc_final: 0.8423 (t80) REVERT: Y 45 GLU cc_start: 0.8487 (tp30) cc_final: 0.8259 (tp30) REVERT: Y 53 ARG cc_start: 0.6489 (ptp-110) cc_final: 0.6279 (ptp-110) REVERT: Z 15 GLU cc_start: 0.6807 (pp20) cc_final: 0.6577 (pp20) REVERT: 1 9 MET cc_start: 0.5871 (ptp) cc_final: 0.4800 (tmm) REVERT: 1 17 PHE cc_start: 0.8354 (m-80) cc_final: 0.8046 (m-80) REVERT: 1 27 LEU cc_start: 0.9107 (tp) cc_final: 0.8870 (tp) REVERT: 1 37 SER cc_start: 0.8365 (p) cc_final: 0.8113 (p) REVERT: 2 13 THR cc_start: 0.6964 (p) cc_final: 0.6597 (t) REVERT: 2 14 ASP cc_start: 0.6618 (m-30) cc_final: 0.6236 (m-30) REVERT: 2 21 HIS cc_start: 0.8004 (t-170) cc_final: 0.7254 (t-170) REVERT: 7 9 MET cc_start: 0.5985 (mtm) cc_final: 0.4457 (mtt) REVERT: 7 14 ARG cc_start: 0.7644 (mtp180) cc_final: 0.7004 (mpp80) REVERT: 7 36 LEU cc_start: 0.8012 (tt) cc_final: 0.7709 (tt) REVERT: 7 42 ASN cc_start: 0.7431 (t0) cc_final: 0.6888 (t0) REVERT: 8 15 GLU cc_start: 0.7078 (tp30) cc_final: 0.6626 (tp30) REVERT: 8 18 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7522 (tm-30) REVERT: 4 34 ILE cc_start: 0.8897 (mt) cc_final: 0.8329 (tp) REVERT: t 18 GLN cc_start: 0.7762 (tp-100) cc_final: 0.7526 (mt0) REVERT: t 24 TYR cc_start: 0.7758 (t80) cc_final: 0.7098 (t80) REVERT: t 29 TRP cc_start: 0.7274 (m100) cc_final: 0.6779 (m100) REVERT: 6 5 TYR cc_start: 0.6071 (p90) cc_final: 0.5202 (p90) REVERT: 5 43 TYR cc_start: 0.7456 (t80) cc_final: 0.6983 (t80) REVERT: C 6 LYS cc_start: 0.7660 (mppt) cc_final: 0.6322 (mmmt) REVERT: C 43 TRP cc_start: 0.8581 (p90) cc_final: 0.8228 (p90) REVERT: L 167 PHE cc_start: 0.6170 (t80) cc_final: 0.5669 (t80) REVERT: M 75 TRP cc_start: 0.4483 (m100) cc_final: 0.4071 (m-10) REVERT: M 184 ASP cc_start: 0.5755 (t0) cc_final: 0.5319 (m-30) REVERT: M 250 LEU cc_start: 0.4501 (mt) cc_final: 0.4271 (mt) REVERT: M 272 MET cc_start: 0.3146 (ttm) cc_final: 0.2878 (tpp) REVERT: H 195 MET cc_start: 0.6061 (tpt) cc_final: 0.5671 (mmt) outliers start: 1 outliers final: 0 residues processed: 741 average time/residue: 0.2945 time to fit residues: 350.5048 Evaluate side-chains 689 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 689 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 14 optimal weight: 0.0040 chunk 147 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 16 GLN ** M 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.186749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.151076 restraints weight = 41828.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.154480 restraints weight = 39867.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154290 restraints weight = 20865.750| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23139 Z= 0.123 Angle : 0.722 47.815 32182 Z= 0.334 Chirality : 0.039 0.199 3297 Planarity : 0.004 0.055 3861 Dihedral : 8.661 89.761 3057 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.17), residues: 2405 helix: 1.85 (0.13), residues: 1566 sheet: 1.29 (1.40), residues: 10 loop : -1.14 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP J 45 HIS 0.011 0.001 HIS B 21 PHE 0.043 0.001 PHE 1 11 TYR 0.024 0.001 TYR G 24 ARG 0.012 0.001 ARG M 228 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 1286) hydrogen bonds : angle 3.99844 ( 3765) covalent geometry : bond 0.00273 (23119) covalent geometry : angle 0.72199 (32182) Misc. bond : bond 0.00084 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 765 time to evaluate : 2.123 Fit side-chains revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6894 (ptp90) cc_final: 0.6164 (mtm180) REVERT: A 40 SER cc_start: 0.7614 (p) cc_final: 0.7160 (t) REVERT: A 52 ASN cc_start: 0.6861 (m-40) cc_final: 0.5813 (t0) REVERT: B 25 MET cc_start: 0.7547 (mmm) cc_final: 0.7235 (mmm) REVERT: D 34 ILE cc_start: 0.8295 (tp) cc_final: 0.8093 (tp) REVERT: F 20 GLN cc_start: 0.6661 (tm-30) cc_final: 0.6357 (tm-30) REVERT: F 42 ASN cc_start: 0.6550 (t0) cc_final: 0.6032 (t0) REVERT: G 46 ARG cc_start: 0.7246 (ttm-80) cc_final: 0.6638 (ttm-80) REVERT: I 3 LYS cc_start: 0.7618 (mmtp) cc_final: 0.6341 (tptp) REVERT: I 8 TRP cc_start: 0.8687 (m100) cc_final: 0.8479 (m100) REVERT: I 43 TRP cc_start: 0.8244 (p90) cc_final: 0.8042 (p90) REVERT: J 16 GLN cc_start: 0.7030 (mt0) cc_final: 0.6354 (mp10) REVERT: J 21 HIS cc_start: 0.8321 (t70) cc_final: 0.7757 (t70) REVERT: J 29 TRP cc_start: 0.8030 (m100) cc_final: 0.7569 (m-10) REVERT: K 1 MET cc_start: 0.3798 (mmm) cc_final: 0.3469 (mmm) REVERT: K 4 PHE cc_start: 0.8337 (m-10) cc_final: 0.8075 (m-80) REVERT: N 10 THR cc_start: 0.9065 (p) cc_final: 0.8656 (p) REVERT: N 25 MET cc_start: 0.8569 (mmm) cc_final: 0.8262 (mmm) REVERT: Q 1 MET cc_start: 0.2956 (ptt) cc_final: 0.2239 (ptm) REVERT: Q 7 ILE cc_start: 0.7244 (mm) cc_final: 0.6978 (mm) REVERT: Q 31 ILE cc_start: 0.8983 (mt) cc_final: 0.8772 (mt) REVERT: R 10 THR cc_start: 0.7528 (p) cc_final: 0.6965 (t) REVERT: S 17 PHE cc_start: 0.8038 (m-80) cc_final: 0.6627 (t80) REVERT: S 34 ILE cc_start: 0.8981 (mt) cc_final: 0.8716 (mm) REVERT: U 6 LYS cc_start: 0.7424 (mttp) cc_final: 0.6895 (mmmt) REVERT: U 12 ASP cc_start: 0.7352 (t70) cc_final: 0.7103 (t70) REVERT: U 15 ARG cc_start: 0.6524 (ptt180) cc_final: 0.6215 (mtt90) REVERT: V 15 GLU cc_start: 0.7769 (pm20) cc_final: 0.7514 (pm20) REVERT: W 15 ARG cc_start: 0.6657 (mpt90) cc_final: 0.5467 (mtm110) REVERT: W 30 MET cc_start: 0.7728 (ttm) cc_final: 0.7187 (ttm) REVERT: W 33 LEU cc_start: 0.8760 (mp) cc_final: 0.8518 (mt) REVERT: X 14 ASP cc_start: 0.7797 (m-30) cc_final: 0.7578 (m-30) REVERT: Y 14 ARG cc_start: 0.6976 (mtp180) cc_final: 0.6291 (mtp85) REVERT: Y 25 PHE cc_start: 0.8680 (t80) cc_final: 0.8450 (t80) REVERT: Y 50 LYS cc_start: 0.7888 (ptmm) cc_final: 0.7301 (pttt) REVERT: Z 15 GLU cc_start: 0.6818 (pp20) cc_final: 0.6570 (pp20) REVERT: 1 27 LEU cc_start: 0.9102 (tp) cc_final: 0.8862 (tp) REVERT: 1 37 SER cc_start: 0.8363 (p) cc_final: 0.8086 (p) REVERT: 2 13 THR cc_start: 0.7090 (p) cc_final: 0.6796 (t) REVERT: 2 14 ASP cc_start: 0.6665 (m-30) cc_final: 0.6392 (m-30) REVERT: 2 21 HIS cc_start: 0.7979 (t-170) cc_final: 0.7417 (t-170) REVERT: 7 9 MET cc_start: 0.5877 (mtm) cc_final: 0.4391 (mtt) REVERT: 7 36 LEU cc_start: 0.8001 (tt) cc_final: 0.7693 (tt) REVERT: 7 42 ASN cc_start: 0.7353 (t0) cc_final: 0.6879 (t0) REVERT: 8 12 LEU cc_start: 0.7668 (mm) cc_final: 0.7349 (mm) REVERT: 8 15 GLU cc_start: 0.7195 (tp30) cc_final: 0.6912 (tp30) REVERT: 8 18 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7569 (tm-30) REVERT: 4 34 ILE cc_start: 0.8901 (mt) cc_final: 0.8348 (tp) REVERT: t 18 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7568 (mt0) REVERT: t 29 TRP cc_start: 0.7228 (m100) cc_final: 0.6779 (m100) REVERT: 6 5 TYR cc_start: 0.6067 (p90) cc_final: 0.5040 (p90) REVERT: 5 43 TYR cc_start: 0.7306 (t80) cc_final: 0.6839 (t80) REVERT: C 6 LYS cc_start: 0.7630 (mppt) cc_final: 0.6370 (mmmt) REVERT: C 43 TRP cc_start: 0.8538 (p90) cc_final: 0.8203 (p90) REVERT: L 167 PHE cc_start: 0.6116 (t80) cc_final: 0.5563 (t80) REVERT: M 75 TRP cc_start: 0.4373 (m100) cc_final: 0.3870 (m-10) REVERT: M 168 MET cc_start: 0.1200 (ptp) cc_final: 0.0445 (pmm) REVERT: M 184 ASP cc_start: 0.5752 (t0) cc_final: 0.5145 (m-30) REVERT: M 250 LEU cc_start: 0.4669 (mt) cc_final: 0.4416 (mt) REVERT: H 195 MET cc_start: 0.6213 (tpt) cc_final: 0.5909 (mmt) REVERT: H 228 LEU cc_start: 0.3900 (tp) cc_final: 0.3509 (pp) outliers start: 0 outliers final: 0 residues processed: 765 average time/residue: 0.2854 time to fit residues: 351.5463 Evaluate side-chains 701 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 701 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 219 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 154 optimal weight: 0.3980 chunk 45 optimal weight: 10.0000 chunk 231 optimal weight: 0.0670 chunk 206 optimal weight: 0.9990 chunk 193 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 21 HIS ** 0 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 52 ASN ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 16 GLN ** M 219 HIS ** 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 = 0.4271 r_free = 0.4271 target = 0.188547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.153707 restraints weight = 41146.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.158398 restraints weight = 48386.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.157364 restraints weight = 25293.323| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 23139 Z= 0.118 Angle : 0.706 47.907 32182 Z= 0.327 Chirality : 0.039 0.195 3297 Planarity : 0.004 0.059 3861 Dihedral : 8.538 89.634 3057 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.17), residues: 2405 helix: 1.88 (0.13), residues: 1564 sheet: 1.40 (1.38), residues: 10 loop : -1.10 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP J 45 HIS 0.011 0.001 HIS B 21 PHE 0.041 0.001 PHE 6 17 TYR 0.020 0.001 TYR 8 24 ARG 0.011 0.001 ARG Q 15 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 1286) hydrogen bonds : angle 3.95264 ( 3765) covalent geometry : bond 0.00259 (23119) covalent geometry : angle 0.70622 (32182) Misc. bond : bond 0.00059 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8374.92 seconds wall clock time: 146 minutes 47.55 seconds (8807.55 seconds total)