Starting phenix.real_space_refine on Sat Jul 4 19:01:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7voy_32062/07_2026/7voy_32062.cif Found real_map, /net/cci-nas-00/data/ceres_data/7voy_32062/07_2026/7voy_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_32062/07_2026/7voy_32062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7voy_32062/07_2026/7voy_32062.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7voy_32062/07_2026/7voy_32062.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7voy_32062/07_2026/7voy_32062.cif" model { file = "/net/cci-nas-00/data/ceres_data/7voy_32062/07_2026/7voy_32062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7voy_32062/07_2026/7voy_32062.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'BCL:plan_0002': 1, 'BPH:plan-1': 1, 'U10:plan-2': 1, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 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: 98 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'BCL:plan_0002': 3, 'BPH:plan-1': 1, 'U10:plan-2': 1, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 63 Time building chain proxies: 3.87, per 1000 atoms: 0.17 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: 2.29 Conformation dependent library (CDL) restraints added in 626.6 milliseconds 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: 0.30 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: 2.90 Time building geometry restraints manager: 2.84 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 - 17.41: 10849 17.41 - 34.82: 873 34.82 - 52.23: 212 52.23 - 69.65: 42 69.65 - 87.06: 32 Dihedral angle restraints: 12008 sinusoidal: 4801 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 12005 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 101) selection = chain '2' selection = (chain '3' and resid 10 through 101) selection = (chain '5' and resid 10 through 101) selection = (chain '8' and resid 10 through 101) selection = (chain 'B' and resid 10 through 101) selection = (chain 'E' and resid 10 through 101) selection = (chain 'G' and resid 10 through 101) selection = (chain 'J' and resid 10 through 101) selection = (chain 'N' and resid 10 through 101) selection = (chain 'P' and resid 10 through 101) selection = (chain 'R' and resid 10 through 101) selection = (chain 'T' and resid 10 through 101) selection = (chain 'V' and resid 10 through 101) selection = (chain 'X' and resid 10 through 101) selection = (chain 'Z' and resid 10 through 101) selection = (chain 't' and resid 10 through 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.640 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 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 : 14.409 87.057 7370 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.79 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 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 ARG 0.006 0.001 ARG A 53 TYR 0.028 0.002 TYR 3 9 PHE 0.024 0.002 PHE Q 11 TRP 0.025 0.002 TRP Y 8 HIS 0.006 0.001 HIS M 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00870 / 0.39 (23119) covalent geometry : angle 0.97475 / 0.45 (32182) hydrogen bonds : bond 0.18077 / 12.39 ( 1286) hydrogen bonds : angle 6.28482 / 4.65 ( 3765) Misc. bond : bond 0.51459 / 32.13 ( 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 : 0.768 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: 0.3618 (p) REVERT: B 16 GLN cc_start: 0.7510 (mt0) cc_final: 0.7184 (mt0) REVERT: F 12 ASP cc_start: 0.8225 (t0) cc_final: 0.7924 (t0) REVERT: G 29 TRP cc_start: 0.8038 (m100) cc_final: 0.7630 (m100) REVERT: G 43 TYR cc_start: 0.8078 (t80) cc_final: 0.6942 (t80) REVERT: I 42 ASN cc_start: 0.8056 (t0) cc_final: 0.7731 (t0) REVERT: J 16 GLN cc_start: 0.6962 (mt0) cc_final: 0.6375 (mm110) REVERT: J 21 HIS cc_start: 0.8479 (t70) cc_final: 0.7726 (t70) REVERT: J 29 TRP cc_start: 0.7827 (m100) cc_final: 0.7447 (m-10) REVERT: K 50 LYS cc_start: 0.7740 (tttt) cc_final: 0.7489 (ttpt) REVERT: O 15 ARG cc_start: 0.6181 (ttp-170) cc_final: 0.4454 (ttp80) REVERT: Q 1 MET cc_start: 0.3661 (ptt) cc_final: 0.3213 (ttp) REVERT: Q 7 ILE cc_start: 0.7347 (mm) cc_final: 0.7035 (mm) REVERT: Q 35 LEU cc_start: 0.9244 (mp) cc_final: 0.8987 (mp) REVERT: R 12 LEU cc_start: 0.8810 (mp) cc_final: 0.8420 (mp) REVERT: S 17 PHE cc_start: 0.8087 (m-80) cc_final: 0.7865 (m-80) REVERT: S 34 ILE cc_start: 0.9057 (mt) cc_final: 0.8754 (mm) REVERT: W 43 TRP cc_start: 0.8344 (p90) cc_final: 0.7922 (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: 0.7710 (ttt) REVERT: Z 16 GLN cc_start: 0.6422 (mt0) cc_final: 0.5996 (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: 0.4694 (ttt) REVERT: 1 14 ARG cc_start: 0.7281 (mpt-90) cc_final: 0.7045 (ptp-170) REVERT: 2 13 THR cc_start: 0.7550 (p) cc_final: 0.7267 (p) REVERT: 2 14 ASP cc_start: 0.6785 (m-30) cc_final: 0.6193 (m-30) REVERT: 2 24 TYR cc_start: 0.7778 (t80) cc_final: 0.7534 (t80) REVERT: 7 14 ARG cc_start: 0.8024 (mtm180) cc_final: 0.7677 (mtp180) REVERT: 7 24 LEU cc_start: 0.7966 (mt) cc_final: 0.7733 (mt) REVERT: 8 18 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7089 (tm-30) REVERT: 8 29 TRP cc_start: 0.7471 (m100) cc_final: 0.7040 (m100) REVERT: 0 39 HIS cc_start: 0.6810 (m90) cc_final: 0.6322 (m90) REVERT: 0 42 VAL cc_start: 0.9325 (t) cc_final: 0.9030 (p) REVERT: 4 9 MET cc_start: 0.6555 (tpt) cc_final: 0.5890 (tpt) REVERT: t 13 THR cc_start: 0.6909 (p) cc_final: 0.6626 (p) REVERT: t 15 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6452 (mt-10) REVERT: t 18 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7095 (mt0) REVERT: t 24 TYR cc_start: 0.7598 (t80) cc_final: 0.7229 (t80) REVERT: t 29 TRP cc_start: 0.7143 (m100) cc_final: 0.6824 (m100) REVERT: t 46 ARG cc_start: 0.6905 (ttm170) cc_final: 0.5296 (tpt-90) REVERT: 6 5 TYR cc_start: 0.6837 (p90) cc_final: 0.6408 (p90) REVERT: 5 21 HIS cc_start: 0.8324 (t70) cc_final: 0.7947 (t-170) REVERT: C 3 LYS cc_start: 0.8110 (mptt) cc_final: 0.7654 (mmmt) REVERT: C 6 LYS cc_start: 0.7628 (mppt) cc_final: 0.6617 (mmmt) REVERT: C 15 ARG cc_start: 0.6013 (mmt180) cc_final: 0.5350 (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: 0.7268 (mt-10) REVERT: 3 25 MET cc_start: 0.7582 (mmm) cc_final: 0.7195 (tpp) REVERT: L 91 ILE cc_start: 0.4555 (mt) cc_final: 0.3998 (tp) REVERT: M 18 LEU cc_start: 0.5806 (mt) cc_final: 0.5382 (mt) REVERT: M 65 MET cc_start: 0.2725 (tpp) cc_final: 0.2494 (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: 0.5068 (t0) REVERT: M 235 LEU cc_start: 0.5340 (tp) cc_final: 0.4763 (tp) REVERT: M 236 GLU cc_start: 0.4928 (mp0) cc_final: 0.4406 (pm20) REVERT: M 272 MET cc_start: 0.3477 (ttm) cc_final: 0.2945 (tpp) outliers start: 26 outliers final: 2 residues processed: 877 average time/residue: 0.1321 time to fit residues: 183.5202 Evaluate side-chains 711 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 707 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN U 20 GLN W 20 GLN Z 18 GLN 0 16 GLN ** t 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 52 ASN C 20 GLN ** L 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.185384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.148468 restraints weight = 41562.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.150228 restraints weight = 33983.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.150946 restraints weight = 18529.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.150766 restraints weight = 14401.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.151151 restraints weight = 13556.875| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23139 Z= 0.173 Angle : 0.765 47.801 32182 Z= 0.360 Chirality : 0.041 0.270 3297 Planarity : 0.005 0.054 3861 Dihedral : 8.904 86.836 2981 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.19 % Allowed : 4.51 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.17), residues: 2405 helix: 2.10 (0.13), residues: 1539 sheet: -1.78 (0.98), residues: 20 loop : -0.97 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 189 TYR 0.016 0.002 TYR P 9 PHE 0.025 0.002 PHE 1 11 TRP 0.031 0.002 TRP L 156 HIS 0.008 0.001 HIS L 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (23119) covalent geometry : angle 0.76457 / 0.36 (32182) hydrogen bonds : bond 0.05557 / 3.75 ( 1286) hydrogen bonds : angle 4.44888 / 3.25 ( 3765) Misc. bond : bond 0.00370 / 0.24 ( 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 810 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 806 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.7579 (m-10) cc_final: 0.7344 (m-10) REVERT: A 40 SER cc_start: 0.7238 (p) cc_final: 0.6586 (t) REVERT: A 41 TYR cc_start: 0.5539 (t80) cc_final: 0.5256 (t80) REVERT: A 51 TYR cc_start: 0.6594 (m-10) cc_final: 0.6220 (m-10) REVERT: A 52 ASN cc_start: 0.6784 (m-40) cc_final: 0.5671 (t0) REVERT: B 21 HIS cc_start: 0.8288 (t-90) cc_final: 0.8020 (t-90) REVERT: G 24 TYR cc_start: 0.7503 (t80) cc_final: 0.7195 (t80) REVERT: G 29 TRP cc_start: 0.7980 (m100) cc_final: 0.7768 (m100) REVERT: J 13 THR cc_start: 0.7802 (p) cc_final: 0.7601 (t) REVERT: J 21 HIS cc_start: 0.8647 (t70) cc_final: 0.7831 (t70) REVERT: J 29 TRP cc_start: 0.7959 (m100) cc_final: 0.7551 (m-10) REVERT: N 25 MET cc_start: 0.8771 (mmm) cc_final: 0.8286 (mmm) REVERT: O 15 ARG cc_start: 0.6236 (ptm-80) cc_final: 0.5733 (mtm110) REVERT: Q 1 MET cc_start: 0.3378 (ptt) cc_final: 0.2922 (ttp) REVERT: Q 7 ILE cc_start: 0.7331 (mm) cc_final: 0.6956 (mm) REVERT: Q 23 PHE cc_start: 0.8381 (t80) cc_final: 0.8119 (t80) REVERT: Q 35 LEU cc_start: 0.9209 (mp) cc_final: 0.8973 (mp) REVERT: Q 51 TYR cc_start: 0.8393 (m-80) cc_final: 0.8116 (m-80) REVERT: R 12 LEU cc_start: 0.8779 (mp) cc_final: 0.8418 (mp) REVERT: S 13 PRO cc_start: 0.8351 (Cg_endo) cc_final: 0.7908 (Cg_exo) REVERT: S 34 ILE cc_start: 0.8914 (mt) cc_final: 0.8592 (mm) REVERT: U 6 LYS cc_start: 0.7788 (mttp) cc_final: 0.7042 (mmtm) REVERT: W 43 TRP cc_start: 0.8515 (p90) cc_final: 0.7852 (p90) REVERT: X 42 VAL cc_start: 0.8506 (t) cc_final: 0.8216 (p) REVERT: Y 45 GLU cc_start: 0.8561 (tp30) cc_final: 0.8266 (tp30) REVERT: Z 29 TRP cc_start: 0.7901 (m100) cc_final: 0.7307 (m100) REVERT: 1 14 ARG cc_start: 0.7432 (mpt-90) cc_final: 0.7195 (ptp-170) REVERT: 2 13 THR cc_start: 0.7629 (p) cc_final: 0.7231 (t) REVERT: 2 14 ASP cc_start: 0.6858 (m-30) cc_final: 0.6514 (m-30) REVERT: 2 20 LEU cc_start: 0.8498 (tp) cc_final: 0.8284 (tp) REVERT: 2 32 SER cc_start: 0.8755 (m) cc_final: 0.8431 (m) REVERT: 7 36 LEU cc_start: 0.8104 (tt) cc_final: 0.7727 (tt) REVERT: 7 42 ASN cc_start: 0.7514 (t0) cc_final: 0.6926 (t0) REVERT: 8 12 LEU cc_start: 0.8093 (mm) cc_final: 0.7852 (mm) REVERT: 8 15 GLU cc_start: 0.7419 (tp30) cc_final: 0.6966 (tp30) REVERT: 8 18 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7160 (tm-30) REVERT: 8 25 MET cc_start: 0.8426 (mmm) cc_final: 0.7635 (mmm) REVERT: 8 29 TRP cc_start: 0.7640 (m100) cc_final: 0.7129 (m100) REVERT: 4 34 ILE cc_start: 0.8782 (mt) cc_final: 0.8287 (tp) REVERT: t 15 GLU cc_start: 0.7604 (mp0) cc_final: 0.7296 (mt-10) REVERT: t 18 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7129 (mt0) REVERT: t 29 TRP cc_start: 0.7261 (m100) cc_final: 0.6867 (m100) REVERT: 6 5 TYR cc_start: 0.6195 (p90) cc_final: 0.5871 (p90) REVERT: 5 21 HIS cc_start: 0.8589 (t70) cc_final: 0.8128 (t70) REVERT: 5 25 MET cc_start: 0.8468 (mmp) cc_final: 0.8262 (mmp) REVERT: 5 42 VAL cc_start: 0.8710 (m) cc_final: 0.8465 (p) REVERT: L 217 ARG cc_start: 0.5365 (mtp180) cc_final: 0.4910 (mtp180) REVERT: M 18 LEU cc_start: 0.5513 (mt) cc_final: 0.5029 (mt) REVERT: M 144 LYS cc_start: 0.2392 (mppt) cc_final: 0.2167 (mmpt) REVERT: M 236 GLU cc_start: 0.5102 (mp0) cc_final: 0.4834 (pt0) REVERT: M 256 MET cc_start: 0.6035 (mmp) cc_final: 0.5511 (ptm) REVERT: M 272 MET cc_start: 0.3452 (ttm) cc_final: 0.2559 (tpp) REVERT: H 173 GLU cc_start: 0.5338 (mp0) cc_final: 0.4520 (pm20) outliers start: 4 outliers final: 0 residues processed: 807 average time/residue: 0.1387 time to fit residues: 179.9588 Evaluate side-chains 705 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 705 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN 1 20 GLN 0 18 GLN 6 52 ASN M 46 GLN M 237 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.184178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140338 restraints weight = 41957.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143782 restraints weight = 20956.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145448 restraints weight = 14081.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.146950 restraints weight = 11658.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.147338 restraints weight = 10169.482| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 23139 Z= 0.178 Angle : 0.751 47.296 32182 Z= 0.350 Chirality : 0.040 0.204 3297 Planarity : 0.004 0.054 3861 Dihedral : 8.713 82.742 2981 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.19 % Allowed : 3.16 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.17), residues: 2405 helix: 1.94 (0.13), residues: 1539 sheet: -1.38 (1.02), residues: 20 loop : -0.94 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 14 TYR 0.017 0.002 TYR 8 24 PHE 0.036 0.002 PHE L 179 TRP 0.018 0.002 TRP L 262 HIS 0.010 0.001 HIS X 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (23119) covalent geometry : angle 0.75131 / 0.35 (32182) hydrogen bonds : bond 0.05053 / 3.40 ( 1286) hydrogen bonds : angle 4.23109 / 3.07 ( 3765) Misc. bond : bond 0.00146 / 0.08 ( 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 790 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 786 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6649 (ptp90) cc_final: 0.6215 (mtm180) REVERT: A 40 SER cc_start: 0.7619 (p) cc_final: 0.7042 (t) REVERT: A 41 TYR cc_start: 0.5685 (t80) cc_final: 0.5366 (t80) REVERT: B 21 HIS cc_start: 0.8386 (t-90) cc_final: 0.8119 (t-90) REVERT: D 51 TYR cc_start: 0.7101 (m-10) cc_final: 0.6871 (m-10) REVERT: F 15 ARG cc_start: 0.6598 (mmt90) cc_final: 0.6056 (ttm-80) REVERT: G 24 TYR cc_start: 0.7766 (t80) cc_final: 0.7559 (t80) REVERT: G 29 TRP cc_start: 0.8071 (m100) cc_final: 0.7835 (m100) REVERT: I 3 LYS cc_start: 0.7626 (mmtp) cc_final: 0.6379 (tptp) REVERT: J 12 LEU cc_start: 0.6924 (mm) cc_final: 0.6311 (mm) REVERT: J 16 GLN cc_start: 0.7577 (mt0) cc_final: 0.6628 (mm110) REVERT: J 21 HIS cc_start: 0.8716 (t70) cc_final: 0.7775 (t70) REVERT: J 29 TRP cc_start: 0.8101 (m100) cc_final: 0.7634 (m-10) REVERT: K 1 MET cc_start: 0.3514 (mmm) cc_final: 0.2632 (tpt) REVERT: N 25 MET cc_start: 0.8790 (mmm) cc_final: 0.8406 (mmm) REVERT: O 6 LYS cc_start: 0.8014 (mmtm) cc_final: 0.7762 (mmtm) REVERT: Q 1 MET cc_start: 0.3240 (ptt) cc_final: 0.2923 (ttp) REVERT: Q 7 ILE cc_start: 0.7358 (mm) cc_final: 0.7056 (mm) REVERT: Q 23 PHE cc_start: 0.8459 (t80) cc_final: 0.8198 (t80) REVERT: Q 35 LEU cc_start: 0.9124 (mp) cc_final: 0.8911 (mp) REVERT: Q 51 TYR cc_start: 0.8413 (m-80) cc_final: 0.8038 (m-80) REVERT: R 12 LEU cc_start: 0.8682 (mp) cc_final: 0.8074 (mp) REVERT: S 13 PRO cc_start: 0.8259 (Cg_endo) cc_final: 0.7859 (Cg_exo) REVERT: S 34 ILE cc_start: 0.8926 (mt) cc_final: 0.8621 (mm) REVERT: T 15 GLU cc_start: 0.8047 (pt0) cc_final: 0.7773 (tp30) REVERT: T 25 MET cc_start: 0.8364 (mmm) cc_final: 0.8154 (mmm) REVERT: U 6 LYS cc_start: 0.7603 (mttp) cc_final: 0.6996 (mmtm) REVERT: U 12 ASP cc_start: 0.7878 (t70) cc_final: 0.7523 (t70) REVERT: W 15 ARG cc_start: 0.7180 (mpt90) cc_final: 0.5840 (ptt90) REVERT: W 27 LEU cc_start: 0.9254 (tp) cc_final: 0.8919 (tp) REVERT: W 43 TRP cc_start: 0.8466 (p90) cc_final: 0.7886 (p90) REVERT: X 14 ASP cc_start: 0.8143 (m-30) cc_final: 0.7929 (m-30) REVERT: X 42 VAL cc_start: 0.8516 (t) cc_final: 0.8235 (p) REVERT: Y 45 GLU cc_start: 0.8594 (tp30) cc_final: 0.8261 (tp30) REVERT: Z 15 GLU cc_start: 0.6987 (pp20) cc_final: 0.6612 (pp20) REVERT: 1 11 PHE cc_start: 0.7545 (t80) cc_final: 0.7085 (t80) REVERT: 1 14 ARG cc_start: 0.7496 (mpt-90) cc_final: 0.7273 (ptp-170) REVERT: 1 15 ARG cc_start: 0.6297 (mtp-110) cc_final: 0.6074 (ttp-110) REVERT: 1 20 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: 2 13 THR cc_start: 0.7592 (p) cc_final: 0.7246 (t) REVERT: 2 14 ASP cc_start: 0.6835 (m-30) cc_final: 0.6476 (m-30) REVERT: 2 32 SER cc_start: 0.8763 (m) cc_final: 0.8521 (m) REVERT: 7 15 ARG cc_start: 0.7702 (mtt-85) cc_final: 0.7323 (tpp-160) REVERT: 7 24 LEU cc_start: 0.7837 (mt) cc_final: 0.7634 (mt) REVERT: 7 36 LEU cc_start: 0.7902 (tt) cc_final: 0.7544 (tt) REVERT: 7 42 ASN cc_start: 0.7544 (t0) cc_final: 0.6985 (t0) REVERT: 8 15 GLU cc_start: 0.7244 (tp30) cc_final: 0.6750 (tp30) REVERT: 8 18 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7328 (tm-30) REVERT: 8 25 MET cc_start: 0.8376 (mmm) cc_final: 0.7823 (mmm) REVERT: 8 29 TRP cc_start: 0.7748 (m100) cc_final: 0.7157 (m100) REVERT: 4 34 ILE cc_start: 0.8861 (mt) cc_final: 0.8343 (tp) REVERT: t 15 GLU cc_start: 0.7570 (mp0) cc_final: 0.7260 (mt-10) REVERT: t 18 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7137 (mt0) REVERT: t 29 TRP cc_start: 0.7244 (m100) cc_final: 0.6836 (m100) REVERT: 6 5 TYR cc_start: 0.6267 (p90) cc_final: 0.6015 (p90) REVERT: 5 21 HIS cc_start: 0.8595 (t70) cc_final: 0.8219 (t70) REVERT: 5 25 MET cc_start: 0.8449 (mmp) cc_final: 0.8198 (mmm) REVERT: C 6 LYS cc_start: 0.7770 (mppt) cc_final: 0.6442 (mmmt) REVERT: C 15 ARG cc_start: 0.5781 (mmm160) cc_final: 0.5312 (mmm160) REVERT: C 43 TRP cc_start: 0.8712 (p90) cc_final: 0.8254 (p90) REVERT: M 18 LEU cc_start: 0.5284 (mt) cc_final: 0.4925 (mt) REVERT: M 236 GLU cc_start: 0.5001 (mp0) cc_final: 0.4623 (pt0) REVERT: M 250 LEU cc_start: 0.4171 (mt) cc_final: 0.3968 (mt) REVERT: M 256 MET cc_start: 0.6072 (mmp) cc_final: 0.5790 (mmp) REVERT: M 272 MET cc_start: 0.2880 (ttm) cc_final: 0.2168 (tpp) REVERT: H 173 GLU cc_start: 0.5639 (mp0) cc_final: 0.4505 (pm20) REVERT: H 175 MET cc_start: 0.3583 (ptt) cc_final: 0.3171 (ptt) outliers start: 4 outliers final: 0 residues processed: 786 average time/residue: 0.1317 time to fit residues: 166.8362 Evaluate side-chains 714 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 713 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 51 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS 0 18 GLN 4 52 ASN 6 52 ASN ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.181977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.145679 restraints weight = 42435.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.147365 restraints weight = 38438.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147784 restraints weight = 23018.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147795 restraints weight = 16926.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.148248 restraints weight = 15757.634| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 23139 Z= 0.241 Angle : 0.827 47.121 32182 Z= 0.386 Chirality : 0.043 0.206 3297 Planarity : 0.005 0.055 3861 Dihedral : 9.011 86.227 2981 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.19 % Allowed : 4.41 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.17), residues: 2405 helix: 1.51 (0.12), residues: 1559 sheet: -1.34 (1.04), residues: 20 loop : -1.15 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 46 TYR 0.019 0.002 TYR M 198 PHE 0.033 0.003 PHE L 179 TRP 0.038 0.002 TRP J 45 HIS 0.010 0.002 HIS X 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 (23119) covalent geometry : angle 0.82652 / 0.39 (32182) hydrogen bonds : bond 0.05203 / 3.48 ( 1286) hydrogen bonds : angle 4.37915 / 3.20 ( 3765) Misc. bond : bond 0.00273 / 0.17 ( 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 769 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 765 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6645 (ptp90) cc_final: 0.6088 (mtm180) REVERT: A 40 SER cc_start: 0.7492 (p) cc_final: 0.6873 (t) REVERT: B 21 HIS cc_start: 0.8491 (t-90) cc_final: 0.8275 (t-90) REVERT: D 34 ILE cc_start: 0.7955 (tp) cc_final: 0.7580 (tp) REVERT: E 15 GLU cc_start: 0.6773 (mp0) cc_final: 0.6572 (mp0) REVERT: E 25 MET cc_start: 0.7090 (mmm) cc_final: 0.6864 (mmm) REVERT: F 15 ARG cc_start: 0.6652 (mmt90) cc_final: 0.6137 (ttm-80) REVERT: F 42 ASN cc_start: 0.7153 (t0) cc_final: 0.6313 (t0) REVERT: G 15 GLU cc_start: 0.7561 (mp0) cc_final: 0.7303 (mp0) REVERT: G 43 TYR cc_start: 0.8275 (t80) cc_final: 0.7900 (t80) REVERT: J 16 GLN cc_start: 0.7733 (mt0) cc_final: 0.7473 (mm-40) REVERT: J 21 HIS cc_start: 0.8609 (t70) cc_final: 0.7897 (t70) REVERT: J 29 TRP cc_start: 0.8026 (m100) cc_final: 0.7577 (m-10) REVERT: K 1 MET cc_start: 0.3611 (mmm) cc_final: 0.3105 (mmm) REVERT: Q 1 MET cc_start: 0.3214 (ptt) cc_final: 0.2975 (ptt) REVERT: Q 7 ILE cc_start: 0.7296 (mm) cc_final: 0.7045 (mm) REVERT: Q 35 LEU cc_start: 0.9269 (mp) cc_final: 0.9043 (mp) REVERT: R 10 THR cc_start: 0.7407 (p) cc_final: 0.6836 (t) REVERT: R 12 LEU cc_start: 0.8595 (mp) cc_final: 0.8091 (mp) REVERT: S 17 PHE cc_start: 0.8149 (m-80) cc_final: 0.7901 (m-80) REVERT: U 6 LYS cc_start: 0.7686 (mttp) cc_final: 0.7075 (mmtm) REVERT: U 12 ASP cc_start: 0.7813 (t70) cc_final: 0.7562 (t70) REVERT: W 15 ARG cc_start: 0.7135 (mpt90) cc_final: 0.5717 (ptm-80) REVERT: W 30 MET cc_start: 0.7735 (ttm) cc_final: 0.7393 (ttm) REVERT: W 43 TRP cc_start: 0.8610 (p90) cc_final: 0.8041 (p90) REVERT: X 42 VAL cc_start: 0.8504 (t) cc_final: 0.8288 (p) REVERT: Y 25 PHE cc_start: 0.8736 (t80) cc_final: 0.8476 (t80) REVERT: Y 45 GLU cc_start: 0.8643 (tp30) cc_final: 0.8350 (tp30) REVERT: Z 15 GLU cc_start: 0.6876 (pp20) cc_final: 0.6492 (pp20) REVERT: 1 9 MET cc_start: 0.5466 (ptp) cc_final: 0.4483 (ttt) REVERT: 1 11 PHE cc_start: 0.7423 (t80) cc_final: 0.7139 (t80) REVERT: 1 14 ARG cc_start: 0.7421 (mpt-90) cc_final: 0.7098 (ptp-170) REVERT: 1 15 ARG cc_start: 0.6349 (mtp-110) cc_final: 0.6079 (ttp-110) REVERT: 2 14 ASP cc_start: 0.6982 (m-30) cc_final: 0.6512 (m-30) REVERT: 2 20 LEU cc_start: 0.8678 (tp) cc_final: 0.8453 (tp) REVERT: 7 9 MET cc_start: 0.6137 (ptp) cc_final: 0.5505 (mtt) REVERT: 7 14 ARG cc_start: 0.7761 (mtp180) cc_final: 0.7109 (mpp80) REVERT: 7 36 LEU cc_start: 0.8003 (tt) cc_final: 0.7638 (tt) REVERT: 7 42 ASN cc_start: 0.7509 (t0) cc_final: 0.6976 (t0) REVERT: 8 15 GLU cc_start: 0.7214 (tp30) cc_final: 0.6834 (tp30) REVERT: 8 18 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7386 (tm-30) REVERT: 8 25 MET cc_start: 0.8364 (mmm) cc_final: 0.7762 (mmm) REVERT: 8 29 TRP cc_start: 0.7745 (m100) cc_final: 0.7210 (m100) REVERT: 4 34 ILE cc_start: 0.8914 (mt) cc_final: 0.8386 (tp) REVERT: t 15 GLU cc_start: 0.7489 (mp0) cc_final: 0.7131 (mt-10) REVERT: t 18 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7096 (mt0) REVERT: t 29 TRP cc_start: 0.7344 (m100) cc_final: 0.6901 (m100) REVERT: 5 25 MET cc_start: 0.8427 (mmp) cc_final: 0.8164 (mmp) REVERT: 5 43 TYR cc_start: 0.7136 (t80) cc_final: 0.6555 (t80) REVERT: C 43 TRP cc_start: 0.8638 (p90) cc_final: 0.8119 (p90) REVERT: 3 12 LEU cc_start: 0.8322 (tp) cc_final: 0.8041 (tp) REVERT: L 217 ARG cc_start: 0.4861 (mtp180) cc_final: 0.4575 (mtp180) REVERT: M 101 TYR cc_start: 0.5490 (m-80) cc_final: 0.5271 (m-80) REVERT: M 142 MET cc_start: 0.3911 (mmt) cc_final: 0.3692 (mmm) REVERT: M 272 MET cc_start: 0.3673 (ttm) cc_final: 0.2672 (tpp) outliers start: 4 outliers final: 0 residues processed: 765 average time/residue: 0.1304 time to fit residues: 161.9501 Evaluate side-chains 697 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 697 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.0050 chunk 69 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 0.0470 chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** L 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.186391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.151233 restraints weight = 41663.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.154630 restraints weight = 37725.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153688 restraints weight = 26409.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.153917 restraints weight = 16380.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.156864 restraints weight = 14847.497| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23139 Z= 0.122 Angle : 0.694 47.958 32182 Z= 0.322 Chirality : 0.038 0.160 3297 Planarity : 0.004 0.053 3861 Dihedral : 8.468 86.658 2981 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.17), residues: 2405 helix: 1.91 (0.13), residues: 1553 sheet: 1.41 (1.58), residues: 10 loop : -1.03 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 15 TYR 0.016 0.001 TYR 8 24 PHE 0.037 0.001 PHE 1 11 TRP 0.014 0.001 TRP 0 48 HIS 0.009 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (23119) covalent geometry : angle 0.69420 / 0.32 (32182) hydrogen bonds : bond 0.04580 / 3.06 ( 1286) hydrogen bonds : angle 4.04019 / 2.93 ( 3765) Misc. bond : bond 0.00093 / 0.05 ( 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 792 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 789 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 SER cc_start: 0.7542 (p) cc_final: 0.7019 (t) REVERT: B 14 ASP cc_start: 0.6156 (p0) cc_final: 0.5889 (t0) REVERT: D 34 ILE cc_start: 0.8014 (tp) cc_final: 0.7679 (tp) REVERT: E 25 MET cc_start: 0.7134 (mmm) cc_final: 0.6900 (mmm) REVERT: F 15 ARG cc_start: 0.6614 (mmt90) cc_final: 0.6105 (ttm-80) REVERT: F 42 ASN cc_start: 0.6950 (t0) cc_final: 0.6263 (t0) REVERT: G 43 TYR cc_start: 0.8145 (t80) cc_final: 0.7936 (t80) REVERT: I 3 LYS cc_start: 0.7680 (mmtp) cc_final: 0.6409 (tptp) REVERT: I 43 TRP cc_start: 0.8286 (p90) cc_final: 0.8063 (p90) REVERT: J 16 GLN cc_start: 0.7499 (mt0) cc_final: 0.6536 (mm110) REVERT: J 21 HIS cc_start: 0.8346 (t70) cc_final: 0.7927 (t70) REVERT: J 29 TRP cc_start: 0.7942 (m100) cc_final: 0.7512 (m-10) REVERT: K 1 MET cc_start: 0.3810 (mmm) cc_final: 0.3334 (mmm) REVERT: K 45 GLU cc_start: 0.6694 (pp20) cc_final: 0.6360 (tm-30) REVERT: N 25 MET cc_start: 0.8605 (mmm) cc_final: 0.8300 (mmm) REVERT: O 6 LYS cc_start: 0.7995 (mmtm) cc_final: 0.7744 (mmtm) REVERT: Q 1 MET cc_start: 0.2960 (ptt) cc_final: 0.2234 (ptm) REVERT: Q 7 ILE cc_start: 0.7224 (mm) cc_final: 0.7003 (mm) REVERT: Q 51 TYR cc_start: 0.8422 (m-80) cc_final: 0.8097 (m-10) REVERT: R 10 THR cc_start: 0.7209 (p) cc_final: 0.6603 (t) REVERT: R 12 LEU cc_start: 0.8558 (mp) cc_final: 0.7983 (mp) REVERT: S 17 PHE cc_start: 0.7977 (m-80) cc_final: 0.7570 (m-80) REVERT: S 34 ILE cc_start: 0.9013 (mt) cc_final: 0.8712 (mm) REVERT: U 6 LYS cc_start: 0.7380 (mttp) cc_final: 0.6962 (mmmt) REVERT: U 12 ASP cc_start: 0.7463 (t70) cc_final: 0.7016 (t70) REVERT: W 15 ARG cc_start: 0.7186 (mpt90) cc_final: 0.5808 (ptm-80) REVERT: W 30 MET cc_start: 0.7779 (ttm) cc_final: 0.7517 (ttm) REVERT: X 42 VAL cc_start: 0.8406 (t) cc_final: 0.8144 (p) REVERT: Y 25 PHE cc_start: 0.8720 (t80) cc_final: 0.8490 (t80) REVERT: Z 15 GLU cc_start: 0.6857 (pp20) cc_final: 0.6497 (pp20) REVERT: 1 37 SER cc_start: 0.8481 (p) cc_final: 0.8280 (p) REVERT: 2 13 THR cc_start: 0.7021 (p) cc_final: 0.6600 (t) REVERT: 2 14 ASP cc_start: 0.6677 (m-30) cc_final: 0.6253 (m-30) REVERT: 7 9 MET cc_start: 0.6257 (ptp) cc_final: 0.5491 (mtt) REVERT: 7 14 ARG cc_start: 0.7609 (mtp180) cc_final: 0.6974 (mpp80) REVERT: 7 36 LEU cc_start: 0.7920 (tt) cc_final: 0.7644 (tt) REVERT: 7 42 ASN cc_start: 0.7400 (t0) cc_final: 0.6900 (t0) REVERT: 8 14 ASP cc_start: 0.7504 (m-30) cc_final: 0.7271 (m-30) REVERT: 8 15 GLU cc_start: 0.7126 (tp30) cc_final: 0.6771 (tp30) REVERT: 8 18 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7455 (tm-30) REVERT: 4 10 ILE cc_start: 0.7420 (pt) cc_final: 0.6854 (mt) REVERT: 4 34 ILE cc_start: 0.8856 (mt) cc_final: 0.8312 (tp) REVERT: t 15 GLU cc_start: 0.7522 (mp0) cc_final: 0.7242 (mt-10) REVERT: t 24 TYR cc_start: 0.7673 (t80) cc_final: 0.7416 (t80) REVERT: t 29 TRP cc_start: 0.7321 (m100) cc_final: 0.6834 (m100) REVERT: 6 5 TYR cc_start: 0.6081 (p90) cc_final: 0.5398 (p90) REVERT: 5 43 TYR cc_start: 0.7070 (t80) cc_final: 0.6643 (t80) REVERT: C 6 LYS cc_start: 0.7458 (mppt) cc_final: 0.6230 (mmmt) REVERT: C 15 ARG cc_start: 0.5894 (mmm160) cc_final: 0.5506 (mmm160) REVERT: C 43 TRP cc_start: 0.8585 (p90) cc_final: 0.8240 (p90) REVERT: L 217 ARG cc_start: 0.4886 (mtp180) cc_final: 0.4601 (mtp180) REVERT: M 142 MET cc_start: 0.3911 (mmt) cc_final: 0.3688 (mmm) REVERT: M 182 HIS cc_start: 0.5888 (t70) cc_final: 0.5391 (t-90) REVERT: M 184 ASP cc_start: 0.5789 (t0) cc_final: 0.5509 (m-30) REVERT: M 272 MET cc_start: 0.3418 (ttm) cc_final: 0.2586 (tpp) outliers start: 3 outliers final: 0 residues processed: 789 average time/residue: 0.1396 time to fit residues: 177.8092 Evaluate side-chains 706 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 706 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 155 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 77 optimal weight: 0.0270 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 52 ASN ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.183324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148420 restraints weight = 42218.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150027 restraints weight = 43434.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149690 restraints weight = 30493.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.150721 restraints weight = 20036.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.151091 restraints weight = 17312.548| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23139 Z= 0.185 Angle : 0.760 47.376 32182 Z= 0.349 Chirality : 0.040 0.171 3297 Planarity : 0.004 0.059 3861 Dihedral : 8.593 84.145 2981 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.17), residues: 2405 helix: 1.77 (0.13), residues: 1556 sheet: 0.68 (1.50), residues: 10 loop : -1.10 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 15 TYR 0.015 0.002 TYR X 9 PHE 0.024 0.002 PHE M 90 TRP 0.016 0.001 TRP W 43 HIS 0.013 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (23119) covalent geometry : angle 0.75988 / 0.35 (32182) hydrogen bonds : bond 0.04679 / 3.13 ( 1286) hydrogen bonds : angle 4.11294 / 3.00 ( 3765) Misc. bond : bond 0.00208 / 0.12 ( 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 751 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 751 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6967 (ptp90) cc_final: 0.6324 (mtm180) REVERT: A 40 SER cc_start: 0.7495 (p) cc_final: 0.6971 (t) REVERT: D 20 GLN cc_start: 0.8444 (pt0) cc_final: 0.8143 (pt0) REVERT: D 34 ILE cc_start: 0.8076 (tp) cc_final: 0.7767 (tp) REVERT: E 25 MET cc_start: 0.7102 (mmm) cc_final: 0.6653 (mmm) REVERT: F 15 ARG cc_start: 0.6836 (mmt90) cc_final: 0.6310 (ttm-80) REVERT: F 42 ASN cc_start: 0.7083 (t0) cc_final: 0.6365 (t0) REVERT: G 15 GLU cc_start: 0.7250 (mp0) cc_final: 0.6980 (mp0) REVERT: G 24 TYR cc_start: 0.7705 (t80) cc_final: 0.7503 (t80) REVERT: G 43 TYR cc_start: 0.8258 (t80) cc_final: 0.7998 (t80) REVERT: I 3 LYS cc_start: 0.7708 (mmtp) cc_final: 0.6275 (tptp) REVERT: I 6 LYS cc_start: 0.7672 (pptt) cc_final: 0.7426 (ptmm) REVERT: I 43 TRP cc_start: 0.8415 (p90) cc_final: 0.8098 (p90) REVERT: J 16 GLN cc_start: 0.7726 (mt0) cc_final: 0.6692 (mm110) REVERT: J 21 HIS cc_start: 0.8653 (t70) cc_final: 0.7721 (t70) REVERT: J 29 TRP cc_start: 0.8049 (m100) cc_final: 0.7610 (m-10) REVERT: K 1 MET cc_start: 0.3738 (mmm) cc_final: 0.3472 (mmm) REVERT: K 45 GLU cc_start: 0.6847 (pp20) cc_final: 0.6412 (tm-30) REVERT: N 10 THR cc_start: 0.9153 (p) cc_final: 0.8746 (p) REVERT: N 25 MET cc_start: 0.8695 (mmm) cc_final: 0.8337 (mmm) REVERT: Q 1 MET cc_start: 0.3058 (ptt) cc_final: 0.2735 (ptt) REVERT: Q 31 ILE cc_start: 0.9069 (mt) cc_final: 0.8869 (mt) REVERT: Q 35 LEU cc_start: 0.9139 (mp) cc_final: 0.8847 (mp) REVERT: Q 51 TYR cc_start: 0.8408 (m-80) cc_final: 0.8128 (m-10) REVERT: R 10 THR cc_start: 0.7451 (p) cc_final: 0.6877 (t) REVERT: R 12 LEU cc_start: 0.8539 (mp) cc_final: 0.7946 (mp) REVERT: S 17 PHE cc_start: 0.8064 (m-80) cc_final: 0.7837 (m-80) REVERT: S 34 ILE cc_start: 0.9018 (mt) cc_final: 0.8723 (mm) REVERT: U 15 ARG cc_start: 0.6649 (ptt180) cc_final: 0.4971 (ptm-80) REVERT: W 9 MET cc_start: 0.7172 (ptt) cc_final: 0.6962 (ptp) REVERT: W 15 ARG cc_start: 0.7203 (mpt90) cc_final: 0.5698 (mtm110) REVERT: W 30 MET cc_start: 0.7813 (ttm) cc_final: 0.7410 (ttm) REVERT: Y 45 GLU cc_start: 0.8610 (tp30) cc_final: 0.8372 (tp30) REVERT: Z 15 GLU cc_start: 0.6925 (pp20) cc_final: 0.6618 (pp20) REVERT: 1 9 MET cc_start: 0.5298 (ptp) cc_final: 0.4122 (ttt) REVERT: 2 13 THR cc_start: 0.7123 (p) cc_final: 0.6722 (t) REVERT: 2 14 ASP cc_start: 0.6773 (m-30) cc_final: 0.6222 (m-30) REVERT: 7 9 MET cc_start: 0.6558 (ptp) cc_final: 0.5677 (mtt) REVERT: 7 36 LEU cc_start: 0.8006 (tt) cc_final: 0.7659 (tt) REVERT: 7 42 ASN cc_start: 0.7438 (t0) cc_final: 0.6929 (t0) REVERT: 8 15 GLU cc_start: 0.7124 (tp30) cc_final: 0.6713 (tp30) REVERT: 8 18 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7450 (tm-30) REVERT: 0 21 HIS cc_start: 0.8542 (t70) cc_final: 0.8082 (t-170) REVERT: 4 10 ILE cc_start: 0.7502 (pt) cc_final: 0.6930 (mt) REVERT: 4 34 ILE cc_start: 0.8892 (mt) cc_final: 0.8346 (tp) REVERT: t 15 GLU cc_start: 0.7442 (mp0) cc_final: 0.7177 (mt-10) REVERT: t 24 TYR cc_start: 0.7748 (t80) cc_final: 0.7149 (t80) REVERT: t 29 TRP cc_start: 0.7346 (m100) cc_final: 0.6830 (m100) REVERT: 6 5 TYR cc_start: 0.6157 (p90) cc_final: 0.5432 (p90) REVERT: 5 43 TYR cc_start: 0.7196 (t80) cc_final: 0.6349 (t80) REVERT: C 6 LYS cc_start: 0.7741 (mppt) cc_final: 0.6468 (mmmt) REVERT: C 15 ARG cc_start: 0.5894 (mmm160) cc_final: 0.5475 (mmm160) REVERT: C 43 TRP cc_start: 0.8569 (p90) cc_final: 0.8143 (p90) REVERT: L 139 MET cc_start: 0.4432 (mpp) cc_final: 0.4098 (mpp) REVERT: L 217 ARG cc_start: 0.4929 (mtp180) cc_final: 0.4615 (mtp180) REVERT: M 182 HIS cc_start: 0.6328 (t70) cc_final: 0.5658 (t-90) REVERT: M 184 ASP cc_start: 0.5707 (t0) cc_final: 0.5225 (m-30) REVERT: M 250 LEU cc_start: 0.4224 (mt) cc_final: 0.3952 (tp) REVERT: M 272 MET cc_start: 0.3324 (ttm) cc_final: 0.2386 (tpp) outliers start: 0 outliers final: 0 residues processed: 751 average time/residue: 0.1376 time to fit residues: 168.6908 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 : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 166 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 52 ASN ** 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 = 0.4217 r_free = 0.4217 target = 0.183758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.148020 restraints weight = 41781.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.151766 restraints weight = 42987.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151173 restraints weight = 25314.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151365 restraints weight = 17321.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.151824 restraints weight = 15920.788| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23139 Z= 0.164 Angle : 0.747 47.590 32182 Z= 0.346 Chirality : 0.040 0.158 3297 Planarity : 0.004 0.052 3861 Dihedral : 8.615 88.587 2981 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2405 helix: 1.69 (0.13), residues: 1569 sheet: 0.55 (1.45), residues: 10 loop : -1.08 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 15 TYR 0.019 0.002 TYR O 5 PHE 0.033 0.002 PHE H 56 TRP 0.025 0.001 TRP M 73 HIS 0.008 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (23119) covalent geometry : angle 0.74695 / 0.35 (32182) hydrogen bonds : bond 0.04692 / 3.14 ( 1286) hydrogen bonds : angle 4.12869 / 3.01 ( 3765) Misc. bond : bond 0.00177 / 0.11 ( 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 760 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 760 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6983 (ptp90) cc_final: 0.6305 (mtm180) REVERT: A 40 SER cc_start: 0.7419 (p) cc_final: 0.6977 (t) REVERT: D 34 ILE cc_start: 0.8078 (tp) cc_final: 0.7765 (tp) REVERT: E 21 HIS cc_start: 0.8681 (t70) cc_final: 0.8392 (t-90) REVERT: E 25 MET cc_start: 0.7803 (mmm) cc_final: 0.7344 (ptt) REVERT: F 15 ARG cc_start: 0.6803 (mmt90) cc_final: 0.6312 (ttm-80) REVERT: G 43 TYR cc_start: 0.8243 (t80) cc_final: 0.7988 (t80) REVERT: I 3 LYS cc_start: 0.7722 (mmtp) cc_final: 0.6308 (tptp) REVERT: I 43 TRP cc_start: 0.8377 (p90) cc_final: 0.8064 (p90) REVERT: J 16 GLN cc_start: 0.7749 (mt0) cc_final: 0.6618 (mm110) REVERT: J 21 HIS cc_start: 0.8446 (t70) cc_final: 0.7824 (t70) REVERT: J 29 TRP cc_start: 0.8076 (m100) cc_final: 0.7606 (m-10) REVERT: K 1 MET cc_start: 0.3962 (mmm) cc_final: 0.3654 (mmm) REVERT: K 45 GLU cc_start: 0.6868 (pp20) cc_final: 0.6547 (tm-30) REVERT: N 10 THR cc_start: 0.9072 (p) cc_final: 0.8631 (p) REVERT: N 25 MET cc_start: 0.8726 (mmm) cc_final: 0.8370 (mmm) REVERT: O 6 LYS cc_start: 0.7892 (mptt) cc_final: 0.7512 (mppt) REVERT: Q 1 MET cc_start: 0.2941 (ptt) cc_final: 0.2662 (ptt) REVERT: Q 31 ILE cc_start: 0.9055 (mt) cc_final: 0.8831 (mt) REVERT: Q 35 LEU cc_start: 0.9050 (mp) cc_final: 0.8727 (mp) REVERT: R 10 THR cc_start: 0.7408 (p) cc_final: 0.6857 (t) REVERT: R 12 LEU cc_start: 0.8505 (mp) cc_final: 0.7996 (mp) REVERT: S 17 PHE cc_start: 0.8132 (m-80) cc_final: 0.7929 (m-80) REVERT: S 34 ILE cc_start: 0.9007 (mt) cc_final: 0.8735 (mm) REVERT: T 15 GLU cc_start: 0.7827 (pt0) cc_final: 0.7609 (tp30) REVERT: U 9 MET cc_start: 0.7614 (ppp) cc_final: 0.6750 (ppp) REVERT: U 15 ARG cc_start: 0.6705 (ptt180) cc_final: 0.4957 (ptm-80) REVERT: W 15 ARG cc_start: 0.6675 (mpt90) cc_final: 0.5501 (mtm110) REVERT: W 30 MET cc_start: 0.7783 (ttm) cc_final: 0.7327 (ttm) REVERT: X 43 TYR cc_start: 0.7632 (t80) cc_final: 0.7420 (t80) REVERT: Y 45 GLU cc_start: 0.8625 (tp30) cc_final: 0.8394 (tp30) REVERT: Z 15 GLU cc_start: 0.6926 (pp20) cc_final: 0.6639 (pp20) REVERT: 1 17 PHE cc_start: 0.8261 (m-80) cc_final: 0.7955 (m-80) REVERT: 2 13 THR cc_start: 0.7210 (p) cc_final: 0.6858 (t) REVERT: 2 14 ASP cc_start: 0.6652 (m-30) cc_final: 0.6269 (m-30) REVERT: 2 32 SER cc_start: 0.8768 (m) cc_final: 0.8563 (m) REVERT: 7 9 MET cc_start: 0.6800 (ptp) cc_final: 0.5738 (mtt) REVERT: 7 36 LEU cc_start: 0.8026 (tt) cc_final: 0.7696 (tt) REVERT: 7 42 ASN cc_start: 0.7420 (t0) cc_final: 0.6874 (t0) REVERT: 8 15 GLU cc_start: 0.7132 (tp30) cc_final: 0.6731 (tp30) REVERT: 8 18 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7485 (tm-30) REVERT: 4 2 SER cc_start: 0.6785 (m) cc_final: 0.6570 (p) REVERT: 4 10 ILE cc_start: 0.7587 (pt) cc_final: 0.7117 (mt) REVERT: 4 34 ILE cc_start: 0.8903 (mt) cc_final: 0.8348 (tp) REVERT: t 15 GLU cc_start: 0.7428 (mp0) cc_final: 0.7151 (mt-10) REVERT: t 24 TYR cc_start: 0.7656 (t80) cc_final: 0.7342 (t80) REVERT: t 29 TRP cc_start: 0.7362 (m100) cc_final: 0.6873 (m100) REVERT: 6 5 TYR cc_start: 0.5975 (p90) cc_final: 0.5297 (p90) REVERT: 5 43 TYR cc_start: 0.7325 (t80) cc_final: 0.6818 (t80) REVERT: C 6 LYS cc_start: 0.7636 (mppt) cc_final: 0.6405 (mmmt) REVERT: C 15 ARG cc_start: 0.5843 (mmm160) cc_final: 0.5425 (mmm160) REVERT: C 43 TRP cc_start: 0.8560 (p90) cc_final: 0.8212 (p90) REVERT: L 139 MET cc_start: 0.4183 (mpp) cc_final: 0.3873 (mpp) REVERT: L 217 ARG cc_start: 0.5009 (mtp180) cc_final: 0.4681 (mtp180) REVERT: M 75 TRP cc_start: 0.4448 (m100) cc_final: 0.3971 (m-10) REVERT: M 182 HIS cc_start: 0.6157 (t70) cc_final: 0.5399 (t-90) REVERT: M 184 ASP cc_start: 0.5789 (t0) cc_final: 0.5317 (m-30) REVERT: M 250 LEU cc_start: 0.4273 (mt) cc_final: 0.3978 (tp) REVERT: M 272 MET cc_start: 0.3315 (ttm) cc_final: 0.2401 (tpp) outliers start: 0 outliers final: 0 residues processed: 760 average time/residue: 0.1388 time to fit residues: 171.1377 Evaluate side-chains 700 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 700 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 194 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 159 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 95 optimal weight: 0.0770 chunk 204 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.184527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148609 restraints weight = 41999.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.151725 restraints weight = 40568.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.151666 restraints weight = 24509.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.151685 restraints weight = 17248.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153098 restraints weight = 15966.130| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23139 Z= 0.153 Angle : 0.745 47.598 32182 Z= 0.345 Chirality : 0.040 0.197 3297 Planarity : 0.004 0.052 3861 Dihedral : 8.580 86.417 2981 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.17), residues: 2405 helix: 1.73 (0.13), residues: 1557 sheet: 0.61 (1.41), residues: 10 loop : -1.09 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 15 TYR 0.024 0.001 TYR 8 24 PHE 0.037 0.002 PHE 1 11 TRP 0.047 0.001 TRP L 156 HIS 0.010 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (23119) covalent geometry : angle 0.74485 / 0.35 (32182) hydrogen bonds : bond 0.04619 / 3.07 ( 1286) hydrogen bonds : angle 4.11243 / 2.99 ( 3765) Misc. bond : bond 0.00145 / 0.09 ( 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 747 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 747 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6929 (ptp90) cc_final: 0.6230 (mtm180) REVERT: A 40 SER cc_start: 0.7454 (p) cc_final: 0.7000 (t) REVERT: D 34 ILE cc_start: 0.8130 (tp) cc_final: 0.7831 (tp) REVERT: E 21 HIS cc_start: 0.8553 (t70) cc_final: 0.8095 (t70) REVERT: E 25 MET cc_start: 0.7845 (mmm) cc_final: 0.7316 (ptt) REVERT: F 15 ARG cc_start: 0.6802 (mmt90) cc_final: 0.6313 (ttm-80) REVERT: I 3 LYS cc_start: 0.7626 (mmtp) cc_final: 0.6313 (tptp) REVERT: I 43 TRP cc_start: 0.8395 (p90) cc_final: 0.8071 (p90) REVERT: J 16 GLN cc_start: 0.7716 (mt0) cc_final: 0.6651 (mm110) REVERT: J 21 HIS cc_start: 0.8289 (t70) cc_final: 0.7952 (t70) REVERT: J 29 TRP cc_start: 0.8060 (m100) cc_final: 0.7598 (m-10) REVERT: K 1 MET cc_start: 0.4015 (mmm) cc_final: 0.3748 (mmm) REVERT: K 45 GLU cc_start: 0.6852 (pp20) cc_final: 0.6345 (tm-30) REVERT: K 52 ASN cc_start: 0.7510 (m-40) cc_final: 0.7303 (t0) REVERT: N 10 THR cc_start: 0.9083 (p) cc_final: 0.8649 (p) REVERT: N 25 MET cc_start: 0.8765 (mmm) cc_final: 0.8408 (mmm) REVERT: Q 1 MET cc_start: 0.2948 (ptt) cc_final: 0.2214 (ptm) REVERT: Q 7 ILE cc_start: 0.7280 (mm) cc_final: 0.7064 (mm) REVERT: Q 35 LEU cc_start: 0.9049 (mp) cc_final: 0.8817 (mp) REVERT: Q 51 TYR cc_start: 0.8377 (m-80) cc_final: 0.8119 (m-10) REVERT: R 10 THR cc_start: 0.7459 (p) cc_final: 0.6964 (t) REVERT: R 12 LEU cc_start: 0.8496 (mp) cc_final: 0.7984 (mp) REVERT: S 13 PRO cc_start: 0.8271 (Cg_endo) cc_final: 0.7939 (Cg_exo) REVERT: S 17 PHE cc_start: 0.8143 (m-80) cc_final: 0.7924 (m-80) REVERT: S 34 ILE cc_start: 0.8995 (mt) cc_final: 0.8715 (mm) REVERT: T 15 GLU cc_start: 0.7865 (pt0) cc_final: 0.7635 (tp30) REVERT: U 15 ARG cc_start: 0.6484 (ptt180) cc_final: 0.4892 (ptm-80) REVERT: W 15 ARG cc_start: 0.6810 (mpt90) cc_final: 0.5529 (mtm110) REVERT: W 30 MET cc_start: 0.7791 (ttm) cc_final: 0.7420 (ttm) REVERT: Y 45 GLU cc_start: 0.8598 (tp30) cc_final: 0.8372 (tp30) REVERT: Z 15 GLU cc_start: 0.6928 (pp20) cc_final: 0.6647 (pp20) REVERT: 1 9 MET cc_start: 0.5567 (ptp) cc_final: 0.4215 (ttt) REVERT: 1 27 LEU cc_start: 0.9119 (tp) cc_final: 0.8905 (tp) REVERT: 1 37 SER cc_start: 0.8456 (p) cc_final: 0.8220 (p) REVERT: 2 13 THR cc_start: 0.7232 (p) cc_final: 0.6866 (t) REVERT: 2 14 ASP cc_start: 0.6691 (m-30) cc_final: 0.6164 (m-30) REVERT: 7 9 MET cc_start: 0.6734 (ptp) cc_final: 0.5667 (mtt) REVERT: 7 36 LEU cc_start: 0.7991 (tt) cc_final: 0.7644 (tt) REVERT: 7 42 ASN cc_start: 0.7407 (t0) cc_final: 0.6896 (t0) REVERT: 8 15 GLU cc_start: 0.7126 (tp30) cc_final: 0.6632 (tp30) REVERT: 8 18 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7501 (tm-30) REVERT: 4 10 ILE cc_start: 0.7575 (pt) cc_final: 0.7081 (mt) REVERT: 4 34 ILE cc_start: 0.8912 (mt) cc_final: 0.8346 (tp) REVERT: t 15 GLU cc_start: 0.7470 (mp0) cc_final: 0.7252 (mt-10) REVERT: t 24 TYR cc_start: 0.7750 (t80) cc_final: 0.7153 (t80) REVERT: t 29 TRP cc_start: 0.7338 (m100) cc_final: 0.6797 (m100) REVERT: 6 1 MET cc_start: 0.3255 (tmm) cc_final: 0.2653 (tmm) REVERT: 6 5 TYR cc_start: 0.5978 (p90) cc_final: 0.5326 (p90) REVERT: 5 43 TYR cc_start: 0.7392 (t80) cc_final: 0.6888 (t80) REVERT: C 6 LYS cc_start: 0.7599 (mppt) cc_final: 0.6352 (mmmt) REVERT: C 15 ARG cc_start: 0.5787 (mmm160) cc_final: 0.5410 (mmm160) REVERT: C 43 TRP cc_start: 0.8523 (p90) cc_final: 0.8172 (p90) REVERT: L 167 PHE cc_start: 0.6224 (t80) cc_final: 0.5754 (t80) REVERT: L 217 ARG cc_start: 0.4999 (mtp180) cc_final: 0.4695 (mtp180) REVERT: M 182 HIS cc_start: 0.6132 (t70) cc_final: 0.5383 (t-90) REVERT: M 184 ASP cc_start: 0.5778 (t0) cc_final: 0.5313 (m-30) REVERT: M 250 LEU cc_start: 0.4275 (mt) cc_final: 0.3987 (tp) REVERT: M 272 MET cc_start: 0.3286 (ttm) cc_final: 0.2370 (tpp) REVERT: H 228 LEU cc_start: 0.4047 (tp) cc_final: 0.3488 (pp) outliers start: 0 outliers final: 0 residues processed: 747 average time/residue: 0.1401 time to fit residues: 169.7453 Evaluate side-chains 683 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 683 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 189 optimal weight: 30.0000 chunk 152 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 220 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C 20 GLN 3 16 GLN ** L 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 ASN ** 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 = 0.182886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.148162 restraints weight = 41991.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.151888 restraints weight = 47750.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.151625 restraints weight = 25116.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.151775 restraints weight = 18114.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152338 restraints weight = 16458.548| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23139 Z= 0.187 Angle : 0.778 47.445 32182 Z= 0.361 Chirality : 0.041 0.176 3297 Planarity : 0.004 0.052 3861 Dihedral : 8.668 84.368 2981 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2405 helix: 1.67 (0.13), residues: 1552 sheet: 0.34 (1.44), residues: 10 loop : -1.16 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 53 TYR 0.024 0.002 TYR O 5 PHE 0.036 0.002 PHE M 216 TRP 0.033 0.002 TRP J 45 HIS 0.007 0.001 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (23119) covalent geometry : angle 0.77833 / 0.36 (32182) hydrogen bonds : bond 0.04748 / 3.14 ( 1286) hydrogen bonds : angle 4.18935 / 3.05 ( 3765) Misc. bond : bond 0.00207 / 0.13 ( 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 730 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 730 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6966 (ptp90) cc_final: 0.6294 (mtm180) REVERT: A 40 SER cc_start: 0.7503 (p) cc_final: 0.7048 (t) REVERT: D 34 ILE cc_start: 0.8125 (tp) cc_final: 0.7832 (tp) REVERT: D 42 ASN cc_start: 0.6449 (t0) cc_final: 0.6109 (t0) REVERT: D 45 GLU cc_start: 0.6381 (pm20) cc_final: 0.6168 (pm20) REVERT: E 21 HIS cc_start: 0.8528 (t70) cc_final: 0.8085 (t70) REVERT: E 25 MET cc_start: 0.7935 (mmm) cc_final: 0.7402 (ptt) REVERT: F 15 ARG cc_start: 0.6866 (mmt90) cc_final: 0.6318 (ttm-80) REVERT: F 20 GLN cc_start: 0.6111 (tt0) cc_final: 0.5843 (tt0) REVERT: G 24 TYR cc_start: 0.7740 (t80) cc_final: 0.7138 (t80) REVERT: I 3 LYS cc_start: 0.7625 (mmtp) cc_final: 0.6369 (tptp) REVERT: I 43 TRP cc_start: 0.8388 (p90) cc_final: 0.8061 (p90) REVERT: J 16 GLN cc_start: 0.7467 (mt0) cc_final: 0.6612 (mm110) REVERT: J 29 TRP cc_start: 0.8051 (m100) cc_final: 0.7627 (m-10) REVERT: K 1 MET cc_start: 0.3971 (mmm) cc_final: 0.1875 (ppp) REVERT: K 45 GLU cc_start: 0.6945 (pp20) cc_final: 0.6404 (tm-30) REVERT: N 10 THR cc_start: 0.9033 (p) cc_final: 0.8611 (p) REVERT: N 25 MET cc_start: 0.8813 (mmm) cc_final: 0.8443 (mmm) REVERT: Q 7 ILE cc_start: 0.7293 (mm) cc_final: 0.7059 (mm) REVERT: Q 35 LEU cc_start: 0.9074 (mp) cc_final: 0.8857 (mp) REVERT: Q 51 TYR cc_start: 0.8313 (m-80) cc_final: 0.8007 (m-10) REVERT: R 10 THR cc_start: 0.7610 (p) cc_final: 0.7046 (t) REVERT: R 12 LEU cc_start: 0.8461 (mp) cc_final: 0.7854 (mp) REVERT: S 17 PHE cc_start: 0.8143 (m-80) cc_final: 0.7889 (m-80) REVERT: S 34 ILE cc_start: 0.9033 (mt) cc_final: 0.8754 (mm) REVERT: U 15 ARG cc_start: 0.6469 (ptt180) cc_final: 0.4933 (ptm-80) REVERT: W 15 ARG cc_start: 0.6897 (mpt90) cc_final: 0.5595 (mtm110) REVERT: W 30 MET cc_start: 0.7676 (ttm) cc_final: 0.7202 (ttm) REVERT: Y 45 GLU cc_start: 0.8607 (tp30) cc_final: 0.8369 (tp30) REVERT: Y 53 ARG cc_start: 0.6499 (ptp-110) cc_final: 0.6279 (ptp-110) REVERT: Z 15 GLU cc_start: 0.6871 (pp20) cc_final: 0.6568 (pp20) REVERT: 1 9 MET cc_start: 0.5795 (ptp) cc_final: 0.4454 (ttt) REVERT: 1 37 SER cc_start: 0.8472 (p) cc_final: 0.8264 (p) REVERT: 2 13 THR cc_start: 0.7228 (p) cc_final: 0.6884 (t) REVERT: 2 14 ASP cc_start: 0.6673 (m-30) cc_final: 0.6188 (m-30) REVERT: 2 21 HIS cc_start: 0.7991 (t-170) cc_final: 0.7571 (t70) REVERT: 7 9 MET cc_start: 0.6853 (ptp) cc_final: 0.5719 (mtt) REVERT: 7 36 LEU cc_start: 0.7970 (tt) cc_final: 0.7628 (tt) REVERT: 7 42 ASN cc_start: 0.7457 (t0) cc_final: 0.6914 (t0) REVERT: 8 15 GLU cc_start: 0.7128 (tp30) cc_final: 0.6637 (tp30) REVERT: 8 18 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7507 (tm-30) REVERT: 0 25 MET cc_start: 0.8217 (mmm) cc_final: 0.7894 (mmt) REVERT: 4 10 ILE cc_start: 0.7535 (pt) cc_final: 0.7018 (mt) REVERT: 4 34 ILE cc_start: 0.8930 (mt) cc_final: 0.8368 (tp) REVERT: t 24 TYR cc_start: 0.7703 (t80) cc_final: 0.7049 (t80) REVERT: t 29 TRP cc_start: 0.7422 (m100) cc_final: 0.6903 (m100) REVERT: 6 1 MET cc_start: 0.3370 (tmm) cc_final: 0.2780 (tmm) REVERT: 6 5 TYR cc_start: 0.5965 (p90) cc_final: 0.5320 (p90) REVERT: 5 43 TYR cc_start: 0.7387 (t80) cc_final: 0.6828 (t80) REVERT: C 6 LYS cc_start: 0.7637 (mppt) cc_final: 0.6487 (mmmt) REVERT: C 15 ARG cc_start: 0.5838 (mmm160) cc_final: 0.5441 (mmm160) REVERT: C 43 TRP cc_start: 0.8533 (p90) cc_final: 0.8142 (p90) REVERT: L 167 PHE cc_start: 0.6308 (t80) cc_final: 0.5801 (t80) REVERT: L 206 MET cc_start: 0.1460 (mmp) cc_final: 0.0177 (tpp) REVERT: L 217 ARG cc_start: 0.5144 (mtp180) cc_final: 0.4810 (mtp180) REVERT: M 182 HIS cc_start: 0.6117 (t70) cc_final: 0.5405 (t-90) REVERT: M 184 ASP cc_start: 0.5700 (t0) cc_final: 0.5262 (m-30) REVERT: M 250 LEU cc_start: 0.4336 (mt) cc_final: 0.4039 (tp) REVERT: M 272 MET cc_start: 0.3302 (ttm) cc_final: 0.2373 (tpp) outliers start: 0 outliers final: 0 residues processed: 730 average time/residue: 0.1291 time to fit residues: 153.6419 Evaluate side-chains 677 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 677 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 166 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 159 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 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 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 = 0.4191 r_free = 0.4191 target = 0.181411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.146875 restraints weight = 40769.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.150136 restraints weight = 53441.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149936 restraints weight = 25846.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.149763 restraints weight = 21548.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.151381 restraints weight = 17011.567| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23139 Z= 0.179 Angle : 0.779 47.510 32182 Z= 0.363 Chirality : 0.041 0.212 3297 Planarity : 0.004 0.060 3861 Dihedral : 8.632 85.984 2981 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2405 helix: 1.59 (0.12), residues: 1560 sheet: 0.24 (1.47), residues: 10 loop : -1.17 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 53 TYR 0.022 0.002 TYR O 5 PHE 0.048 0.002 PHE 1 17 TRP 0.034 0.002 TRP L 156 HIS 0.011 0.001 HIS 0 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (23119) covalent geometry : angle 0.77900 / 0.36 (32182) hydrogen bonds : bond 0.04791 / 3.17 ( 1286) hydrogen bonds : angle 4.21450 / 3.08 ( 3765) Misc. bond : bond 0.00186 / 0.11 ( 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 735 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 735 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6858 (ptp90) cc_final: 0.6281 (mtm180) REVERT: A 40 SER cc_start: 0.7533 (p) cc_final: 0.7097 (t) REVERT: D 34 ILE cc_start: 0.8141 (tp) cc_final: 0.7842 (tp) REVERT: D 42 ASN cc_start: 0.6413 (t0) cc_final: 0.6099 (t0) REVERT: E 21 HIS cc_start: 0.8425 (t70) cc_final: 0.7989 (t70) REVERT: E 25 MET cc_start: 0.7890 (mmm) cc_final: 0.7465 (ptt) REVERT: F 15 ARG cc_start: 0.6860 (mmt90) cc_final: 0.6338 (ttm-80) REVERT: I 3 LYS cc_start: 0.7643 (mmtp) cc_final: 0.6344 (tptp) REVERT: I 43 TRP cc_start: 0.8402 (p90) cc_final: 0.8067 (p90) REVERT: J 29 TRP cc_start: 0.7966 (m100) cc_final: 0.7603 (m-10) REVERT: K 1 MET cc_start: 0.3615 (mmm) cc_final: 0.1782 (ppp) REVERT: K 45 GLU cc_start: 0.6997 (pp20) cc_final: 0.6502 (tm-30) REVERT: N 10 THR cc_start: 0.9015 (p) cc_final: 0.8570 (p) REVERT: N 25 MET cc_start: 0.8786 (mmm) cc_final: 0.8436 (mmm) REVERT: Q 7 ILE cc_start: 0.7211 (mm) cc_final: 0.6965 (mm) REVERT: Q 26 LEU cc_start: 0.9306 (mt) cc_final: 0.9102 (mt) REVERT: R 10 THR cc_start: 0.7645 (p) cc_final: 0.7181 (t) REVERT: R 12 LEU cc_start: 0.8668 (mp) cc_final: 0.8019 (mp) REVERT: S 13 PRO cc_start: 0.8305 (Cg_endo) cc_final: 0.7791 (Cg_exo) REVERT: S 34 ILE cc_start: 0.9022 (mt) cc_final: 0.8752 (mm) REVERT: U 9 MET cc_start: 0.7630 (ppp) cc_final: 0.6681 (ppp) REVERT: U 15 ARG cc_start: 0.6514 (ptt180) cc_final: 0.6141 (mtt90) REVERT: W 15 ARG cc_start: 0.6849 (mpt90) cc_final: 0.5618 (mtm110) REVERT: W 30 MET cc_start: 0.7693 (ttm) cc_final: 0.7240 (ttm) REVERT: W 33 LEU cc_start: 0.8797 (mp) cc_final: 0.8526 (mt) REVERT: Y 45 GLU cc_start: 0.8576 (tp30) cc_final: 0.8353 (tp30) REVERT: Z 15 GLU cc_start: 0.6836 (pp20) cc_final: 0.6523 (pp20) REVERT: 1 9 MET cc_start: 0.5813 (ptp) cc_final: 0.4498 (ttt) REVERT: 1 27 LEU cc_start: 0.9112 (tp) cc_final: 0.8890 (tp) REVERT: 1 37 SER cc_start: 0.8485 (p) cc_final: 0.8284 (p) REVERT: 2 13 THR cc_start: 0.7135 (p) cc_final: 0.6802 (t) REVERT: 2 14 ASP cc_start: 0.6499 (m-30) cc_final: 0.6056 (m-30) REVERT: 7 9 MET cc_start: 0.6917 (ptp) cc_final: 0.5724 (mtt) REVERT: 7 36 LEU cc_start: 0.7978 (tt) cc_final: 0.7623 (tt) REVERT: 7 42 ASN cc_start: 0.7419 (t0) cc_final: 0.6899 (t0) REVERT: 8 15 GLU cc_start: 0.7077 (tp30) cc_final: 0.6626 (tp30) REVERT: 8 18 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7491 (tm-30) REVERT: 4 10 ILE cc_start: 0.7486 (pt) cc_final: 0.7153 (mt) REVERT: 4 34 ILE cc_start: 0.8911 (mt) cc_final: 0.8344 (tp) REVERT: t 25 MET cc_start: 0.7802 (mmm) cc_final: 0.7525 (mmt) REVERT: t 29 TRP cc_start: 0.7202 (m100) cc_final: 0.6735 (m100) REVERT: 6 1 MET cc_start: 0.3342 (tmm) cc_final: 0.2806 (tmm) REVERT: 6 5 TYR cc_start: 0.5960 (p90) cc_final: 0.5299 (p90) REVERT: 5 43 TYR cc_start: 0.7366 (t80) cc_final: 0.6835 (t80) REVERT: C 6 LYS cc_start: 0.7534 (mppt) cc_final: 0.6427 (mmmt) REVERT: C 15 ARG cc_start: 0.5816 (mmm160) cc_final: 0.5430 (mmm160) REVERT: C 43 TRP cc_start: 0.8549 (p90) cc_final: 0.8192 (p90) REVERT: L 167 PHE cc_start: 0.6338 (t80) cc_final: 0.5813 (t80) REVERT: L 206 MET cc_start: 0.1168 (mmp) cc_final: -0.0099 (tpp) REVERT: L 217 ARG cc_start: 0.5118 (mtp180) cc_final: 0.4759 (mtp180) REVERT: M 140 LEU cc_start: 0.5065 (mp) cc_final: 0.4645 (mp) REVERT: M 168 MET cc_start: 0.1703 (ptp) cc_final: 0.1157 (pmm) REVERT: M 182 HIS cc_start: 0.6156 (t70) cc_final: 0.5621 (t-90) REVERT: M 250 LEU cc_start: 0.4326 (mt) cc_final: 0.4036 (tp) REVERT: M 272 MET cc_start: 0.3381 (ttm) cc_final: 0.2388 (tpp) REVERT: H 228 LEU cc_start: 0.3913 (tp) cc_final: 0.3355 (pp) outliers start: 0 outliers final: 0 residues processed: 735 average time/residue: 0.1357 time to fit residues: 162.0265 Evaluate side-chains 681 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 681 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.183396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149085 restraints weight = 40592.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.152366 restraints weight = 50458.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.151787 restraints weight = 25710.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.151719 restraints weight = 19257.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.152607 restraints weight = 16784.574| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.4247 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 : 0.749 47.650 32182 Z= 0.347 Chirality : 0.040 0.228 3297 Planarity : 0.004 0.057 3861 Dihedral : 8.509 86.590 2981 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2405 helix: 1.63 (0.13), residues: 1574 sheet: -0.63 (1.35), residues: 12 loop : -1.32 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 53 TYR 0.021 0.001 TYR O 5 PHE 0.023 0.002 PHE H 56 TRP 0.035 0.001 TRP L 156 HIS 0.009 0.001 HIS 0 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (23119) covalent geometry : angle 0.74852 / 0.35 (32182) hydrogen bonds : bond 0.04609 / 3.05 ( 1286) hydrogen bonds : angle 4.15858 / 3.03 ( 3765) Misc. bond : bond 0.00145 / 0.09 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3874.11 seconds wall clock time: 67 minutes 50.54 seconds (4070.54 seconds total)