Starting phenix.real_space_refine on Fri Sep 19 03:49:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7voy_32062/09_2025/7voy_32062.cif Found real_map, /net/cci-nas-00/data/ceres_data/7voy_32062/09_2025/7voy_32062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7voy_32062/09_2025/7voy_32062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7voy_32062/09_2025/7voy_32062.map" model { file = "/net/cci-nas-00/data/ceres_data/7voy_32062/09_2025/7voy_32062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7voy_32062/09_2025/7voy_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 76 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: 108 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: 5.51, per 1000 atoms: 0.25 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: 2.21 Conformation dependent library (CDL) restraints added in 767.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.50 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: 3.51 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 - 18.83: 11029 18.83 - 37.65: 811 37.65 - 56.48: 180 56.48 - 75.31: 36 75.31 - 94.13: 28 Dihedral angle restraints: 12084 sinusoidal: 4877 harmonic: 7207 Sorted by residual: dihedral pdb=" CA TYR V 9 " pdb=" C TYR V 9 " pdb=" N THR V 10 " pdb=" CA THR V 10 " ideal model delta harmonic sigma weight residual 180.00 140.79 39.21 0 5.00e+00 4.00e-02 6.15e+01 dihedral pdb=" CA TYR 0 9 " pdb=" C TYR 0 9 " pdb=" N THR 0 10 " pdb=" CA THR 0 10 " ideal model delta harmonic sigma weight residual -180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA TYR P 9 " pdb=" C TYR P 9 " pdb=" N THR P 10 " pdb=" CA THR P 10 " ideal model delta harmonic sigma weight residual 180.00 144.80 35.20 0 5.00e+00 4.00e-02 4.96e+01 ... (remaining 12081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.048: 3296 1.048 - 2.096: 0 2.096 - 3.144: 0 3.144 - 4.192: 0 4.192 - 5.240: 1 Chirality restraints: 3297 Sorted by residual: chirality pdb=" C22 SPN M 407 " pdb=" C21 SPN M 407 " pdb=" C23 SPN M 407 " pdb=" CM7 SPN M 407 " both_signs ideal model delta sigma weight residual False -2.58 2.66 -5.24 2.00e-01 2.50e+01 6.86e+02 chirality pdb=" C3C BPH M 405 " pdb=" C2C BPH M 405 " pdb=" C4C BPH M 405 " pdb=" CAC BPH M 405 " both_signs ideal model delta sigma weight residual False 2.83 2.60 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA TYR P 9 " pdb=" N TYR P 9 " pdb=" C TYR P 9 " pdb=" CB TYR P 9 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3294 not shown) Planarity restraints: 3861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 SPN M 407 " -0.176 2.00e-02 2.50e+03 2.26e-01 6.41e+02 pdb=" C29 SPN M 407 " 0.345 2.00e-02 2.50e+03 pdb=" C30 SPN M 407 " -0.289 2.00e-02 2.50e+03 pdb=" CM9 SPN M 407 " 0.150 2.00e-02 2.50e+03 pdb=" CMB SPN M 407 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 SPN M 407 " -0.094 2.00e-02 2.50e+03 1.68e-01 3.51e+02 pdb=" C7 SPN M 407 " 0.021 2.00e-02 2.50e+03 pdb=" C8 SPN M 407 " -0.132 2.00e-02 2.50e+03 pdb=" C9 SPN M 407 " 0.318 2.00e-02 2.50e+03 pdb=" CM4 SPN M 407 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH M 405 " -0.020 2.00e-02 2.50e+03 1.12e-01 2.80e+02 pdb=" C1D BPH M 405 " -0.029 2.00e-02 2.50e+03 pdb=" C2D BPH M 405 " 0.055 2.00e-02 2.50e+03 pdb=" C3D BPH M 405 " 0.088 2.00e-02 2.50e+03 pdb=" C4D BPH M 405 " 0.071 2.00e-02 2.50e+03 pdb=" CAD BPH M 405 " -0.250 2.00e-02 2.50e+03 pdb=" CHA BPH M 405 " 0.095 2.00e-02 2.50e+03 pdb=" CHD BPH M 405 " -0.113 2.00e-02 2.50e+03 pdb=" CMD BPH M 405 " 0.104 2.00e-02 2.50e+03 ... (remaining 3858 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 302 2.62 - 3.19: 20720 3.19 - 3.76: 36412 3.76 - 4.33: 47449 4.33 - 4.90: 76475 Nonbonded interactions: 181358 Sorted by model distance: nonbonded pdb=" OG1 THR K 38 " pdb=" O SER K 40 " model vdw 2.056 3.040 nonbonded pdb=" OG1 THR L 15 " pdb=" O GLY L 18 " model vdw 2.063 3.040 nonbonded pdb=" O TRP R 48 " pdb=" OG SER S 47 " model vdw 2.066 3.040 nonbonded pdb=" O PRO V 47 " pdb=" NH2 ARG W 53 " model vdw 2.094 3.120 nonbonded pdb=" O TYR L 30 " pdb=" NH2 ARG L 103 " model vdw 2.118 3.120 ... (remaining 181353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 10 through 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.300 Find NCS groups from input model: 0.720 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: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.691 23139 Z= 1.563 Angle : 0.975 49.038 32182 Z= 0.454 Chirality : 0.101 5.240 3297 Planarity : 0.008 0.226 3861 Dihedral : 14.581 94.135 7446 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 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 aren 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 covalent geometry : bond 0.00870 (23119) covalent geometry : angle 0.97475 (32182) hydrogen bonds : bond 0.18077 ( 1286) hydrogen bonds : angle 6.28482 ( 3765) Misc. bond : bond 0.51459 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 865 time to evaluate : 0.961 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: 0.7725 (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: 0.7466 (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: 0.8323 (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: 0.1525 time to fit residues: 211.6293 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 : 1.049 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN U 20 GLN W 20 GLN 0 16 GLN 4 52 ASN 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 = 0.185451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.148927 restraints weight = 41523.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.152460 restraints weight = 35885.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.152253 restraints weight = 19845.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.152090 restraints weight = 14528.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.152772 restraints weight = 13413.625| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23139 Z= 0.167 Angle : 0.765 47.635 32182 Z= 0.360 Chirality : 0.041 0.256 3297 Planarity : 0.005 0.052 3861 Dihedral : 9.335 89.285 3057 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.34 % Allowed : 4.70 % Favored : 94.97 % 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 aren not related in a simple way. whole: 1.49 (0.17), residues: 2405 helix: 2.05 (0.13), residues: 1539 sheet: -1.77 (0.98), residues: 20 loop : -0.98 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 46 TYR 0.017 0.002 TYR W 5 PHE 0.034 0.002 PHE 1 11 TRP 0.029 0.002 TRP L 156 HIS 0.008 0.002 HIS L 211 Details of bonding type rmsd covalent geometry : bond 0.00368 (23119) covalent geometry : angle 0.76541 (32182) hydrogen bonds : bond 0.05351 ( 1286) hydrogen bonds : angle 4.39719 ( 3765) Misc. bond : bond 0.00152 ( 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 820 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 813 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.7563 (m-10) cc_final: 0.7333 (m-10) REVERT: A 14 ARG cc_start: 0.6633 (ptp90) cc_final: 0.6199 (mtm180) REVERT: A 40 SER cc_start: 0.7359 (p) cc_final: 0.6740 (t) REVERT: A 51 TYR cc_start: 0.6586 (m-10) cc_final: 0.6223 (m-10) REVERT: A 52 ASN cc_start: 0.6795 (m-40) cc_final: 0.5674 (t0) REVERT: B 14 ASP cc_start: 0.5799 (t0) cc_final: 0.5441 (t0) REVERT: B 21 HIS cc_start: 0.8265 (t-90) cc_final: 0.8053 (t-90) REVERT: D 44 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8052 (mt) REVERT: J 13 THR cc_start: 0.7880 (p) cc_final: 0.7672 (t) REVERT: J 21 HIS cc_start: 0.8693 (t70) cc_final: 0.7859 (t70) REVERT: J 29 TRP cc_start: 0.7955 (m100) cc_final: 0.7521 (m-10) REVERT: N 25 MET cc_start: 0.8783 (mmm) cc_final: 0.8307 (mmm) REVERT: O 15 ARG cc_start: 0.6137 (ptm-80) cc_final: 0.5619 (mtm180) REVERT: P 19 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: Q 1 MET cc_start: 0.3337 (ptt) cc_final: 0.2927 (ttp) REVERT: Q 7 ILE cc_start: 0.7371 (mm) cc_final: 0.6999 (mm) REVERT: Q 23 PHE cc_start: 0.8428 (t80) cc_final: 0.8171 (t80) REVERT: Q 35 LEU cc_start: 0.9147 (mp) cc_final: 0.8929 (mp) REVERT: Q 51 TYR cc_start: 0.8405 (m-80) cc_final: 0.7937 (m-80) REVERT: R 12 LEU cc_start: 0.8771 (mp) cc_final: 0.8423 (mp) REVERT: S 13 PRO cc_start: 0.8341 (Cg_endo) cc_final: 0.7866 (Cg_exo) REVERT: S 17 PHE cc_start: 0.8091 (m-10) cc_final: 0.7870 (m-80) REVERT: S 34 ILE cc_start: 0.8886 (mt) cc_final: 0.8556 (mm) REVERT: T 25 MET cc_start: 0.7959 (mtp) cc_final: 0.7753 (mmm) REVERT: U 6 LYS cc_start: 0.7798 (mttp) cc_final: 0.7039 (mmtm) REVERT: U 12 ASP cc_start: 0.6991 (t70) cc_final: 0.6439 (t70) REVERT: W 43 TRP cc_start: 0.8534 (p90) cc_final: 0.7893 (p90) REVERT: X 42 VAL cc_start: 0.8545 (t) cc_final: 0.8255 (p) REVERT: Y 45 GLU cc_start: 0.8558 (tp30) cc_final: 0.8226 (tp30) REVERT: 1 14 ARG cc_start: 0.7428 (mpt-90) cc_final: 0.7200 (ptp-170) REVERT: 1 23 PHE cc_start: 0.8612 (t80) cc_final: 0.8174 (t80) REVERT: 2 13 THR cc_start: 0.7689 (p) cc_final: 0.7286 (t) REVERT: 2 14 ASP cc_start: 0.6841 (m-30) cc_final: 0.6529 (m-30) REVERT: 2 32 SER cc_start: 0.8770 (m) cc_final: 0.8447 (m) REVERT: 7 36 LEU cc_start: 0.8042 (tt) cc_final: 0.7668 (tt) REVERT: 7 42 ASN cc_start: 0.7531 (t0) cc_final: 0.6944 (t0) REVERT: 8 12 LEU cc_start: 0.8089 (mm) cc_final: 0.7857 (mm) REVERT: 8 15 GLU cc_start: 0.7424 (tp30) cc_final: 0.7001 (tp30) REVERT: 8 18 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7160 (tm-30) REVERT: 8 25 MET cc_start: 0.8461 (mmm) cc_final: 0.7695 (mmm) REVERT: 8 29 TRP cc_start: 0.7647 (m100) cc_final: 0.7133 (m100) REVERT: 4 34 ILE cc_start: 0.8781 (mt) cc_final: 0.8315 (tp) REVERT: t 15 GLU cc_start: 0.7596 (mp0) cc_final: 0.7279 (mt-10) REVERT: t 18 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7139 (mt0) REVERT: t 29 TRP cc_start: 0.7259 (m100) cc_final: 0.6857 (m100) REVERT: 6 5 TYR cc_start: 0.6148 (p90) cc_final: 0.5848 (p90) REVERT: 5 21 HIS cc_start: 0.8604 (t70) cc_final: 0.8133 (t70) REVERT: 5 42 VAL cc_start: 0.8691 (m) cc_final: 0.8451 (p) REVERT: C 15 ARG cc_start: 0.5820 (mmt180) cc_final: 0.5336 (mmm160) REVERT: C 37 SER cc_start: 0.8702 (m) cc_final: 0.8299 (p) REVERT: L 217 ARG cc_start: 0.5402 (mtp180) cc_final: 0.4960 (mtp180) REVERT: M 18 LEU cc_start: 0.5524 (mt) cc_final: 0.5031 (mt) REVERT: M 144 LYS cc_start: 0.2454 (mppt) cc_final: 0.2199 (mmpt) REVERT: M 236 GLU cc_start: 0.5112 (mp0) cc_final: 0.4870 (pt0) REVERT: M 256 MET cc_start: 0.6068 (mmp) cc_final: 0.5494 (ptm) REVERT: M 272 MET cc_start: 0.3479 (ttm) cc_final: 0.2570 (tpp) REVERT: H 173 GLU cc_start: 0.5330 (mp0) cc_final: 0.4521 (pm20) outliers start: 7 outliers final: 0 residues processed: 815 average time/residue: 0.1406 time to fit residues: 183.8772 Evaluate side-chains 707 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 705 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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: 9.9990 chunk 222 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN 1 20 GLN 0 18 GLN 6 52 ASN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.180824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145905 restraints weight = 41928.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149293 restraints weight = 51162.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.149120 restraints weight = 24437.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.149538 restraints weight = 20547.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149892 restraints weight = 17303.266| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.130 23139 Z= 0.282 Angle : 0.878 46.996 32182 Z= 0.411 Chirality : 0.045 0.240 3297 Planarity : 0.006 0.055 3861 Dihedral : 9.779 88.785 3057 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.14 % Allowed : 5.13 % Favored : 94.73 % 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 aren not related in a simple way. whole: 0.77 (0.17), residues: 2405 helix: 1.42 (0.12), residues: 1555 sheet: -1.27 (1.02), residues: 20 loop : -1.19 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 15 TYR 0.019 0.002 TYR P 9 PHE 0.038 0.003 PHE L 179 TRP 0.026 0.002 TRP F 43 HIS 0.009 0.002 HIS M 202 Details of bonding type rmsd covalent geometry : bond 0.00664 (23119) covalent geometry : angle 0.87801 (32182) hydrogen bonds : bond 0.05521 ( 1286) hydrogen bonds : angle 4.53248 ( 3765) Misc. bond : bond 0.00286 ( 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 767 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 764 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6703 (ptp90) cc_final: 0.6217 (mtm180) REVERT: B 21 HIS cc_start: 0.8501 (t-90) cc_final: 0.8236 (t-90) REVERT: D 34 ILE cc_start: 0.8263 (tp) cc_final: 0.8011 (tp) REVERT: F 15 ARG cc_start: 0.6625 (mmt90) cc_final: 0.6105 (ttm-80) REVERT: G 15 GLU cc_start: 0.7589 (mp0) cc_final: 0.7337 (mp0) REVERT: I 41 TYR cc_start: 0.8678 (m-80) cc_final: 0.8451 (m-80) REVERT: J 16 GLN cc_start: 0.7757 (mt0) cc_final: 0.6960 (mm-40) REVERT: J 21 HIS cc_start: 0.8640 (t70) cc_final: 0.7693 (t70) REVERT: J 29 TRP cc_start: 0.7998 (m100) cc_final: 0.7567 (m-10) REVERT: K 1 MET cc_start: 0.3267 (mmm) cc_final: 0.2885 (mmm) REVERT: Q 1 MET cc_start: 0.3413 (ptt) cc_final: 0.3200 (ptt) REVERT: Q 7 ILE cc_start: 0.7279 (mm) cc_final: 0.7002 (mm) REVERT: Q 26 LEU cc_start: 0.9339 (mt) cc_final: 0.9104 (mt) REVERT: Q 35 LEU cc_start: 0.9211 (mp) cc_final: 0.8979 (mp) REVERT: R 10 THR cc_start: 0.7434 (p) cc_final: 0.6954 (t) REVERT: R 12 LEU cc_start: 0.8548 (mp) cc_final: 0.8072 (mp) REVERT: S 13 PRO cc_start: 0.8332 (Cg_endo) cc_final: 0.7976 (Cg_exo) REVERT: U 6 LYS cc_start: 0.7750 (mttp) cc_final: 0.7154 (mmtm) REVERT: W 15 ARG cc_start: 0.7256 (mpt90) cc_final: 0.5801 (ptt90) REVERT: W 43 TRP cc_start: 0.8673 (p90) cc_final: 0.7836 (p90) REVERT: X 42 VAL cc_start: 0.8522 (t) cc_final: 0.8282 (p) REVERT: Y 26 LEU cc_start: 0.8655 (mp) cc_final: 0.8435 (mp) REVERT: Y 45 GLU cc_start: 0.8642 (tp30) cc_final: 0.8320 (tp30) REVERT: Z 15 GLU cc_start: 0.6803 (pp20) cc_final: 0.6431 (pp20) REVERT: 1 9 MET cc_start: 0.5797 (ptp) cc_final: 0.4600 (ttt) REVERT: 1 11 PHE cc_start: 0.7445 (t80) cc_final: 0.6939 (t80) REVERT: 1 14 ARG cc_start: 0.7483 (mpt-90) cc_final: 0.7099 (ptp-170) REVERT: 1 15 ARG cc_start: 0.6359 (mtp-110) cc_final: 0.6139 (ttp-110) REVERT: 1 16 VAL cc_start: 0.8590 (m) cc_final: 0.8332 (m) REVERT: 2 14 ASP cc_start: 0.6892 (m-30) cc_final: 0.6477 (m-30) REVERT: 2 32 SER cc_start: 0.8901 (m) cc_final: 0.8682 (m) REVERT: 7 9 MET cc_start: 0.5868 (mtm) cc_final: 0.4821 (mtt) REVERT: 7 36 LEU cc_start: 0.8008 (tt) cc_final: 0.7631 (tt) REVERT: 7 42 ASN cc_start: 0.7499 (t0) cc_final: 0.6953 (t0) REVERT: 8 15 GLU cc_start: 0.7095 (tp30) cc_final: 0.6751 (tp30) REVERT: 8 18 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7409 (tm-30) REVERT: 8 25 MET cc_start: 0.8477 (mmm) cc_final: 0.7913 (mmt) REVERT: 8 29 TRP cc_start: 0.7706 (m100) cc_final: 0.7172 (m100) REVERT: 4 34 ILE cc_start: 0.8875 (mt) cc_final: 0.8321 (tp) REVERT: t 15 GLU cc_start: 0.7449 (mp0) cc_final: 0.7055 (mt-10) REVERT: t 18 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7093 (mt0) REVERT: t 29 TRP cc_start: 0.7234 (m100) cc_final: 0.6812 (m100) REVERT: 5 43 TYR cc_start: 0.7092 (t80) cc_final: 0.6766 (t80) REVERT: C 6 LYS cc_start: 0.7704 (mppt) cc_final: 0.6327 (mmmt) REVERT: C 35 LEU cc_start: 0.8343 (tp) cc_final: 0.8098 (tp) REVERT: C 43 TRP cc_start: 0.8647 (p90) cc_final: 0.8161 (p90) REVERT: L 115 TYR cc_start: 0.1803 (m-10) cc_final: 0.1003 (m-80) REVERT: L 217 ARG cc_start: 0.5666 (mtp180) cc_final: 0.5228 (mtp180) REVERT: L 219 LEU cc_start: 0.4012 (tp) cc_final: 0.3791 (tp) REVERT: M 18 LEU cc_start: 0.5646 (mt) cc_final: 0.5423 (mt) REVERT: M 236 GLU cc_start: 0.5047 (mp0) cc_final: 0.4826 (pt0) REVERT: M 272 MET cc_start: 0.3840 (ttm) cc_final: 0.2830 (tpp) outliers start: 3 outliers final: 0 residues processed: 764 average time/residue: 0.1280 time to fit residues: 157.9268 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 : 0.675 ------------------------------------------------------------------------------- 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: 2.9990 chunk 89 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 193 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 20 GLN 0 18 GLN 6 52 ASN ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN H 68 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.182284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.147307 restraints weight = 41671.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149995 restraints weight = 40471.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149558 restraints weight = 26076.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.149869 restraints weight = 17907.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.150522 restraints weight = 16260.143| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.3383 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= 0.165 Angle : 0.745 47.557 32182 Z= 0.346 Chirality : 0.040 0.162 3297 Planarity : 0.004 0.054 3861 Dihedral : 9.339 87.308 3057 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.19 % Allowed : 3.07 % Favored : 96.74 % 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 aren not related in a simple way. whole: 1.07 (0.17), residues: 2405 helix: 1.70 (0.13), residues: 1546 sheet: -1.46 (0.99), residues: 20 loop : -1.14 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 1 14 TYR 0.019 0.002 TYR 8 24 PHE 0.031 0.002 PHE 1 17 TRP 0.019 0.001 TRP L 262 HIS 0.009 0.001 HIS V 21 Details of bonding type rmsd covalent geometry : bond 0.00379 (23119) covalent geometry : angle 0.74483 (32182) hydrogen bonds : bond 0.04931 ( 1286) hydrogen bonds : angle 4.22015 ( 3765) Misc. bond : bond 0.00163 ( 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 785 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 781 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6682 (ptp90) cc_final: 0.6113 (mtm180) REVERT: A 40 SER cc_start: 0.7528 (p) cc_final: 0.6952 (t) REVERT: D 34 ILE cc_start: 0.8377 (tp) cc_final: 0.8158 (tp) REVERT: D 51 TYR cc_start: 0.7098 (m-10) cc_final: 0.6888 (m-10) REVERT: E 25 MET cc_start: 0.7072 (mmm) cc_final: 0.6829 (mmm) REVERT: F 15 ARG cc_start: 0.6755 (mmt90) cc_final: 0.6264 (ttm-80) REVERT: F 42 ASN cc_start: 0.7052 (t0) cc_final: 0.6315 (t0) REVERT: I 43 TRP cc_start: 0.8286 (p90) cc_final: 0.8016 (p90) REVERT: J 21 HIS cc_start: 0.8415 (t70) cc_final: 0.7664 (t70) REVERT: J 29 TRP cc_start: 0.7990 (m100) cc_final: 0.7549 (m-10) REVERT: K 1 MET cc_start: 0.3311 (mmm) cc_final: 0.2994 (mmm) REVERT: N 15 GLU cc_start: 0.7808 (tp30) cc_final: 0.7533 (mp0) REVERT: N 25 MET cc_start: 0.8682 (mmm) cc_final: 0.8396 (mmm) REVERT: Q 1 MET cc_start: 0.3100 (ptt) cc_final: 0.2803 (ptt) REVERT: Q 7 ILE cc_start: 0.7242 (mm) cc_final: 0.6998 (mm) REVERT: R 10 THR cc_start: 0.7378 (p) cc_final: 0.6806 (t) REVERT: R 12 LEU cc_start: 0.8560 (mp) cc_final: 0.8080 (mp) REVERT: S 17 PHE cc_start: 0.8182 (m-80) cc_final: 0.7865 (m-80) REVERT: S 34 ILE cc_start: 0.9037 (mt) cc_final: 0.8732 (mm) REVERT: U 6 LYS cc_start: 0.7665 (mttp) cc_final: 0.6930 (mmtm) REVERT: W 15 ARG cc_start: 0.7211 (mpt90) cc_final: 0.5733 (ptt90) REVERT: W 43 TRP cc_start: 0.8615 (p90) cc_final: 0.8091 (p90) REVERT: X 42 VAL cc_start: 0.8472 (t) cc_final: 0.8264 (p) REVERT: Y 45 GLU cc_start: 0.8604 (tp30) cc_final: 0.8365 (tp30) REVERT: Z 15 GLU cc_start: 0.6904 (pp20) cc_final: 0.6523 (pp20) REVERT: 1 11 PHE cc_start: 0.7450 (t80) cc_final: 0.7144 (t80) REVERT: 1 15 ARG cc_start: 0.6299 (mtp-110) cc_final: 0.6061 (ttp-110) REVERT: 2 13 THR cc_start: 0.7185 (p) cc_final: 0.6850 (t) REVERT: 2 14 ASP cc_start: 0.6827 (m-30) cc_final: 0.6498 (m-30) REVERT: 2 32 SER cc_start: 0.8859 (m) cc_final: 0.8625 (m) REVERT: 7 9 MET cc_start: 0.5840 (mtm) cc_final: 0.5044 (mtt) REVERT: 7 14 ARG cc_start: 0.7706 (mtp180) cc_final: 0.7031 (mpp80) REVERT: 7 36 LEU cc_start: 0.8013 (tt) cc_final: 0.7643 (tt) REVERT: 7 42 ASN cc_start: 0.7473 (t0) cc_final: 0.6949 (t0) REVERT: 8 15 GLU cc_start: 0.7157 (tp30) cc_final: 0.6799 (tp30) REVERT: 8 18 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7323 (tm-30) REVERT: 8 21 HIS cc_start: 0.8098 (t-170) cc_final: 0.7816 (t-170) REVERT: 8 25 MET cc_start: 0.8469 (mmm) cc_final: 0.7574 (mmt) REVERT: 8 29 TRP cc_start: 0.7707 (m100) cc_final: 0.7198 (m100) REVERT: 4 9 MET cc_start: 0.6568 (tpt) cc_final: 0.6274 (tpp) REVERT: 4 10 ILE cc_start: 0.7372 (pt) cc_final: 0.6770 (mt) REVERT: 4 34 ILE cc_start: 0.8875 (mt) cc_final: 0.8335 (tp) REVERT: t 15 GLU cc_start: 0.7494 (mp0) cc_final: 0.7221 (mt-10) REVERT: t 18 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7081 (mt0) REVERT: t 24 TYR cc_start: 0.7811 (t80) cc_final: 0.7100 (t80) REVERT: t 29 TRP cc_start: 0.7382 (m100) cc_final: 0.6917 (m100) REVERT: 6 5 TYR cc_start: 0.6054 (p90) cc_final: 0.5457 (p90) REVERT: 5 43 TYR cc_start: 0.7126 (t80) cc_final: 0.6716 (t80) REVERT: C 6 LYS cc_start: 0.7692 (mppt) cc_final: 0.6384 (mmmt) REVERT: C 15 ARG cc_start: 0.5656 (mmm160) cc_final: 0.5161 (mmm160) REVERT: C 35 LEU cc_start: 0.8296 (tp) cc_final: 0.7943 (tp) REVERT: C 43 TRP cc_start: 0.8596 (p90) cc_final: 0.8185 (p90) REVERT: L 217 ARG cc_start: 0.5493 (mtp180) cc_final: 0.5258 (mtp180) REVERT: M 57 VAL cc_start: 0.3421 (t) cc_final: 0.3213 (t) REVERT: M 168 MET cc_start: 0.1749 (mtm) cc_final: 0.1522 (mtm) REVERT: M 218 MET cc_start: 0.2438 (ptp) cc_final: 0.2038 (ptp) REVERT: M 272 MET cc_start: 0.3482 (ttm) cc_final: 0.2494 (tpp) outliers start: 4 outliers final: 0 residues processed: 781 average time/residue: 0.1302 time to fit residues: 164.0690 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 : 0.761 ------------------------------------------------------------------------------- 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: 0.5980 chunk 69 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 165 optimal weight: 0.0170 chunk 170 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** M 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.182821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.147974 restraints weight = 41602.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.152054 restraints weight = 39958.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.150739 restraints weight = 26403.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.150959 restraints weight = 16065.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.151345 restraints weight = 14231.471| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 23139 Z= 0.149 Angle : 0.729 47.647 32182 Z= 0.337 Chirality : 0.039 0.178 3297 Planarity : 0.004 0.054 3861 Dihedral : 9.088 86.331 3057 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.10 % Allowed : 2.49 % Favored : 97.41 % 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 aren not related in a simple way. whole: 1.23 (0.17), residues: 2405 helix: 1.84 (0.13), residues: 1548 sheet: -1.61 (1.03), residues: 20 loop : -1.13 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 14 TYR 0.018 0.001 TYR O 5 PHE 0.049 0.002 PHE 1 11 TRP 0.017 0.001 TRP L 262 HIS 0.015 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00341 (23119) covalent geometry : angle 0.72876 (32182) hydrogen bonds : bond 0.04690 ( 1286) hydrogen bonds : angle 4.14598 ( 3765) Misc. bond : bond 0.00142 ( 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 757 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 755 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 SER cc_start: 0.7479 (p) cc_final: 0.6938 (t) REVERT: A 51 TYR cc_start: 0.6531 (m-10) cc_final: 0.6274 (m-10) REVERT: D 34 ILE cc_start: 0.8383 (tp) cc_final: 0.8177 (tp) REVERT: D 51 TYR cc_start: 0.7118 (m-10) cc_final: 0.6898 (m-10) REVERT: E 25 MET cc_start: 0.7069 (mmm) cc_final: 0.6842 (mmm) REVERT: F 15 ARG cc_start: 0.6719 (mmt90) cc_final: 0.6231 (ttm-80) REVERT: F 42 ASN cc_start: 0.6988 (t0) cc_final: 0.6287 (t0) REVERT: G 46 ARG cc_start: 0.7072 (ttm-80) cc_final: 0.6763 (ttm-80) REVERT: I 3 LYS cc_start: 0.7713 (mmtp) cc_final: 0.6382 (tptp) REVERT: I 43 TRP cc_start: 0.8388 (p90) cc_final: 0.8005 (p90) REVERT: J 16 GLN cc_start: 0.7366 (mt0) cc_final: 0.7091 (mm-40) REVERT: J 21 HIS cc_start: 0.8398 (t70) cc_final: 0.7922 (t70) REVERT: J 29 TRP cc_start: 0.8019 (m100) cc_final: 0.7544 (m-10) REVERT: K 1 MET cc_start: 0.3795 (mmm) cc_final: 0.3465 (mmm) REVERT: N 10 THR cc_start: 0.9080 (p) cc_final: 0.8656 (p) REVERT: N 25 MET cc_start: 0.8716 (mmm) cc_final: 0.8406 (mmm) REVERT: Q 1 MET cc_start: 0.3078 (ptt) cc_final: 0.2359 (ptm) REVERT: Q 7 ILE cc_start: 0.7261 (mm) cc_final: 0.7034 (mm) REVERT: Q 11 PHE cc_start: 0.7501 (m-80) cc_final: 0.7270 (m-80) REVERT: Q 35 LEU cc_start: 0.9107 (mp) cc_final: 0.8822 (mp) REVERT: Q 51 TYR cc_start: 0.8343 (m-80) cc_final: 0.8003 (m-10) REVERT: R 10 THR cc_start: 0.7410 (p) cc_final: 0.6852 (t) REVERT: R 12 LEU cc_start: 0.8535 (mp) cc_final: 0.8005 (mp) REVERT: S 17 PHE cc_start: 0.8113 (m-80) cc_final: 0.7783 (m-80) REVERT: S 34 ILE cc_start: 0.8965 (mt) cc_final: 0.8672 (mm) REVERT: T 15 GLU cc_start: 0.7855 (pt0) cc_final: 0.7621 (tp30) REVERT: U 6 LYS cc_start: 0.7512 (mttp) cc_final: 0.7052 (mmmt) REVERT: W 15 ARG cc_start: 0.7208 (mpt90) cc_final: 0.5774 (ptm-80) REVERT: W 27 LEU cc_start: 0.9266 (tp) cc_final: 0.8990 (tp) REVERT: X 42 VAL cc_start: 0.8442 (t) cc_final: 0.8234 (p) REVERT: Y 45 GLU cc_start: 0.8655 (tp30) cc_final: 0.8421 (tp30) REVERT: Z 15 GLU cc_start: 0.6912 (pp20) cc_final: 0.6589 (pp20) REVERT: 2 13 THR cc_start: 0.7243 (p) cc_final: 0.6848 (t) REVERT: 2 14 ASP cc_start: 0.6837 (m-30) cc_final: 0.6477 (m-30) REVERT: 7 9 MET cc_start: 0.5917 (mtm) cc_final: 0.5083 (mtt) REVERT: 7 36 LEU cc_start: 0.7949 (tt) cc_final: 0.7653 (tt) REVERT: 7 42 ASN cc_start: 0.7449 (t0) cc_final: 0.6924 (t0) REVERT: 8 15 GLU cc_start: 0.7155 (tp30) cc_final: 0.6728 (tp30) REVERT: 8 18 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7422 (tm-30) REVERT: 8 21 HIS cc_start: 0.8139 (t-170) cc_final: 0.7830 (t-170) REVERT: 0 21 HIS cc_start: 0.8517 (t70) cc_final: 0.8061 (t-170) REVERT: 4 9 MET cc_start: 0.6490 (tpt) cc_final: 0.6184 (tpp) REVERT: 4 10 ILE cc_start: 0.7355 (pt) cc_final: 0.6817 (mt) REVERT: 4 34 ILE cc_start: 0.8893 (mt) cc_final: 0.8330 (tp) REVERT: t 15 GLU cc_start: 0.7581 (mp0) cc_final: 0.7292 (mt-10) REVERT: t 18 GLN cc_start: 0.7799 (tp-100) cc_final: 0.7567 (mt0) REVERT: t 24 TYR cc_start: 0.7613 (t80) cc_final: 0.7270 (t80) REVERT: t 29 TRP cc_start: 0.7354 (m100) cc_final: 0.6858 (m100) REVERT: 6 5 TYR cc_start: 0.6058 (p90) cc_final: 0.5435 (p90) REVERT: 6 17 PHE cc_start: 0.8549 (m-80) cc_final: 0.8219 (m-80) REVERT: 5 43 TYR cc_start: 0.7184 (t80) cc_final: 0.6648 (t80) REVERT: C 6 LYS cc_start: 0.7750 (mppt) cc_final: 0.6543 (mmmt) REVERT: C 15 ARG cc_start: 0.5681 (mmm160) cc_final: 0.5248 (mmm160) REVERT: C 35 LEU cc_start: 0.8328 (tp) cc_final: 0.8128 (tp) REVERT: C 43 TRP cc_start: 0.8604 (p90) cc_final: 0.8204 (p90) REVERT: M 101 TYR cc_start: 0.5710 (m-80) cc_final: 0.5504 (m-80) REVERT: M 182 HIS cc_start: 0.6136 (t-90) cc_final: 0.5394 (t-90) REVERT: M 236 GLU cc_start: 0.4734 (mt-10) cc_final: 0.4440 (pt0) REVERT: M 272 MET cc_start: 0.3313 (ttm) cc_final: 0.2420 (tpp) outliers start: 2 outliers final: 0 residues processed: 755 average time/residue: 0.1319 time to fit residues: 161.2962 Evaluate side-chains 694 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 694 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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: 9.9990 chunk 62 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 223 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** 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 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.183846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.139735 restraints weight = 41818.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142698 restraints weight = 21139.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.144292 restraints weight = 14250.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144733 restraints weight = 11811.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144733 restraints weight = 11119.645| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23139 Z= 0.152 Angle : 0.733 47.618 32182 Z= 0.338 Chirality : 0.040 0.152 3297 Planarity : 0.004 0.053 3861 Dihedral : 8.930 85.785 3057 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.65 % 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 aren not related in a simple way. whole: 1.24 (0.17), residues: 2405 helix: 1.85 (0.13), residues: 1549 sheet: 0.54 (1.52), residues: 10 loop : -1.15 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 15 TYR 0.015 0.001 TYR O 5 PHE 0.025 0.002 PHE 4 4 TRP 0.025 0.001 TRP M 73 HIS 0.009 0.001 HIS 0 21 Details of bonding type rmsd covalent geometry : bond 0.00350 (23119) covalent geometry : angle 0.73280 (32182) hydrogen bonds : bond 0.04664 ( 1286) hydrogen bonds : angle 4.11719 ( 3765) Misc. bond : bond 0.00150 ( 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 752 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 751 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6915 (ptp90) cc_final: 0.6294 (mtm180) REVERT: A 40 SER cc_start: 0.7506 (p) cc_final: 0.7018 (t) REVERT: D 51 TYR cc_start: 0.7155 (m-10) cc_final: 0.6932 (m-10) REVERT: E 25 MET cc_start: 0.7199 (mmm) cc_final: 0.6951 (mmm) REVERT: F 15 ARG cc_start: 0.6719 (mmt90) cc_final: 0.6242 (ttm-80) REVERT: F 42 ASN cc_start: 0.6951 (t0) cc_final: 0.6271 (t0) REVERT: G 46 ARG cc_start: 0.7063 (ttm-80) cc_final: 0.6794 (ttm-80) REVERT: I 3 LYS cc_start: 0.7663 (mmtp) cc_final: 0.6213 (tptp) REVERT: I 43 TRP cc_start: 0.8379 (p90) cc_final: 0.8082 (p90) REVERT: J 13 THR cc_start: 0.7688 (t) cc_final: 0.7322 (t) REVERT: J 16 GLN cc_start: 0.7437 (mt0) cc_final: 0.6556 (mp10) REVERT: J 21 HIS cc_start: 0.8440 (t70) cc_final: 0.8089 (t70) REVERT: J 29 TRP cc_start: 0.8146 (m100) cc_final: 0.7613 (m-10) REVERT: K 1 MET cc_start: 0.4021 (mmm) cc_final: 0.3671 (mmm) REVERT: N 10 THR cc_start: 0.9074 (p) cc_final: 0.8650 (p) REVERT: N 25 MET cc_start: 0.8810 (mmm) cc_final: 0.8407 (mmm) REVERT: Q 1 MET cc_start: 0.2924 (ptt) cc_final: 0.2213 (ptm) REVERT: Q 7 ILE cc_start: 0.7380 (mm) cc_final: 0.7159 (mm) REVERT: Q 11 PHE cc_start: 0.7536 (m-80) cc_final: 0.7146 (m-10) REVERT: Q 35 LEU cc_start: 0.9207 (mp) cc_final: 0.8857 (mp) REVERT: Q 51 TYR cc_start: 0.8345 (m-80) cc_final: 0.8080 (m-10) REVERT: R 10 THR cc_start: 0.7330 (p) cc_final: 0.6849 (t) REVERT: R 12 LEU cc_start: 0.8561 (mp) cc_final: 0.8145 (mp) REVERT: S 17 PHE cc_start: 0.8139 (m-80) cc_final: 0.7827 (m-80) REVERT: S 34 ILE cc_start: 0.9021 (mt) cc_final: 0.8723 (mm) REVERT: T 15 GLU cc_start: 0.8071 (pt0) cc_final: 0.7716 (tp30) REVERT: U 6 LYS cc_start: 0.7481 (mttp) cc_final: 0.6998 (mmmt) REVERT: W 15 ARG cc_start: 0.6801 (mpt90) cc_final: 0.5602 (mtm110) REVERT: X 42 VAL cc_start: 0.8529 (t) cc_final: 0.8303 (p) REVERT: Y 45 GLU cc_start: 0.8613 (tp30) cc_final: 0.8380 (tp30) REVERT: Z 15 GLU cc_start: 0.6979 (pp20) cc_final: 0.6682 (pp20) REVERT: 1 9 MET cc_start: 0.4985 (ptp) cc_final: 0.4098 (ttt) REVERT: 1 27 LEU cc_start: 0.9123 (tp) cc_final: 0.8907 (tp) REVERT: 1 37 SER cc_start: 0.8481 (p) cc_final: 0.8267 (p) REVERT: 2 13 THR cc_start: 0.7249 (p) cc_final: 0.6848 (t) REVERT: 2 14 ASP cc_start: 0.6830 (m-30) cc_final: 0.6217 (m-30) REVERT: 2 32 SER cc_start: 0.8819 (m) cc_final: 0.8599 (m) REVERT: 7 9 MET cc_start: 0.6018 (mtm) cc_final: 0.5149 (mtt) REVERT: 7 36 LEU cc_start: 0.7977 (tt) cc_final: 0.7665 (tt) REVERT: 7 42 ASN cc_start: 0.7542 (t0) cc_final: 0.7003 (t0) REVERT: 8 15 GLU cc_start: 0.7218 (tp30) cc_final: 0.6729 (tp30) REVERT: 8 18 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7378 (tm-30) REVERT: 8 25 MET cc_start: 0.8409 (mmt) cc_final: 0.7362 (mmt) REVERT: 8 29 TRP cc_start: 0.7857 (m100) cc_final: 0.7271 (m100) REVERT: 4 2 SER cc_start: 0.6794 (m) cc_final: 0.6576 (p) REVERT: 4 9 MET cc_start: 0.6578 (tpt) cc_final: 0.6320 (tpp) REVERT: 4 10 ILE cc_start: 0.7452 (pt) cc_final: 0.7035 (mt) REVERT: 4 34 ILE cc_start: 0.8916 (mt) cc_final: 0.8373 (tp) REVERT: t 15 GLU cc_start: 0.7517 (mp0) cc_final: 0.7248 (mt-10) REVERT: t 18 GLN cc_start: 0.7905 (tp-100) cc_final: 0.7603 (mt0) REVERT: t 24 TYR cc_start: 0.7830 (t80) cc_final: 0.7299 (t80) REVERT: t 29 TRP cc_start: 0.7501 (m100) cc_final: 0.6961 (m100) REVERT: 6 5 TYR cc_start: 0.5978 (p90) cc_final: 0.5320 (p90) REVERT: 6 17 PHE cc_start: 0.8733 (m-80) cc_final: 0.8493 (m-80) REVERT: 5 25 MET cc_start: 0.8547 (mmp) cc_final: 0.8319 (mmp) REVERT: 5 43 TYR cc_start: 0.7241 (t80) cc_final: 0.6550 (t80) REVERT: C 6 LYS cc_start: 0.7865 (mppt) cc_final: 0.6623 (mmmt) REVERT: C 15 ARG cc_start: 0.5604 (mmm160) cc_final: 0.5207 (mmm160) REVERT: C 35 LEU cc_start: 0.8326 (tp) cc_final: 0.8116 (tp) REVERT: C 43 TRP cc_start: 0.8642 (p90) cc_final: 0.8298 (p90) REVERT: L 139 MET cc_start: 0.4570 (mpp) cc_final: 0.4262 (mpp) REVERT: L 167 PHE cc_start: 0.5894 (t80) cc_final: 0.5498 (t80) REVERT: L 217 ARG cc_start: 0.4307 (mtp180) cc_final: 0.4072 (mtp180) REVERT: M 182 HIS cc_start: 0.5835 (t-90) cc_final: 0.5219 (t-90) REVERT: M 184 ASP cc_start: 0.5726 (t0) cc_final: 0.5267 (m-30) REVERT: M 198 TYR cc_start: 0.3408 (m-10) cc_final: 0.2780 (m-80) REVERT: M 236 GLU cc_start: 0.3709 (mt-10) cc_final: 0.3344 (pm20) REVERT: M 272 MET cc_start: 0.2605 (ttm) cc_final: 0.1986 (tpp) outliers start: 1 outliers final: 0 residues processed: 752 average time/residue: 0.1354 time to fit residues: 165.6013 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 : 0.778 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 10.0000 chunk 173 optimal weight: 30.0000 chunk 152 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 GLN 2 21 HIS ** 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 ** M 182 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.182905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.147298 restraints weight = 41891.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150386 restraints weight = 39306.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149585 restraints weight = 25138.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.149693 restraints weight = 16074.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.150253 restraints weight = 14617.093| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 23139 Z= 0.183 Angle : 0.760 47.514 32182 Z= 0.352 Chirality : 0.041 0.182 3297 Planarity : 0.004 0.061 3861 Dihedral : 8.941 83.940 3057 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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 aren not related in a simple way. whole: 1.14 (0.17), residues: 2405 helix: 1.76 (0.13), residues: 1551 sheet: 0.51 (1.47), residues: 10 loop : -1.17 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG T 46 TYR 0.025 0.002 TYR 4 51 PHE 0.039 0.002 PHE 1 11 TRP 0.018 0.001 TRP M 73 HIS 0.009 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00427 (23119) covalent geometry : angle 0.75982 (32182) hydrogen bonds : bond 0.04735 ( 1286) hydrogen bonds : angle 4.14397 ( 3765) Misc. bond : bond 0.00191 ( 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 739 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 739 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6992 (ptp90) cc_final: 0.6379 (mtm180) REVERT: A 40 SER cc_start: 0.7502 (p) cc_final: 0.6940 (t) REVERT: A 41 TYR cc_start: 0.6327 (t80) cc_final: 0.6047 (t80) REVERT: D 34 ILE cc_start: 0.8309 (tp) cc_final: 0.8104 (tp) REVERT: F 15 ARG cc_start: 0.6831 (mmt90) cc_final: 0.6336 (ttm-80) REVERT: F 42 ASN cc_start: 0.7050 (t0) cc_final: 0.6358 (t0) REVERT: G 46 ARG cc_start: 0.7036 (ttm-80) cc_final: 0.6748 (ttm-80) REVERT: I 3 LYS cc_start: 0.7653 (mmtp) cc_final: 0.6341 (tptp) REVERT: I 43 TRP cc_start: 0.8395 (p90) cc_final: 0.8045 (p90) REVERT: J 16 GLN cc_start: 0.7257 (mt0) cc_final: 0.6643 (mp10) REVERT: J 21 HIS cc_start: 0.8580 (t70) cc_final: 0.7668 (t70) REVERT: J 29 TRP cc_start: 0.8102 (m100) cc_final: 0.7622 (m-10) REVERT: K 1 MET cc_start: 0.3715 (mmm) cc_final: 0.1951 (ppp) REVERT: N 10 THR cc_start: 0.9115 (p) cc_final: 0.8657 (p) REVERT: N 25 MET cc_start: 0.8859 (mmm) cc_final: 0.8519 (mmm) REVERT: Q 7 ILE cc_start: 0.7297 (mm) cc_final: 0.7077 (mm) REVERT: Q 11 PHE cc_start: 0.7644 (m-80) cc_final: 0.7294 (m-80) REVERT: Q 35 LEU cc_start: 0.9147 (mp) cc_final: 0.8926 (mp) REVERT: Q 51 TYR cc_start: 0.8391 (m-80) cc_final: 0.8141 (m-10) REVERT: R 10 THR cc_start: 0.7528 (p) cc_final: 0.7003 (t) REVERT: R 12 LEU cc_start: 0.8489 (mp) cc_final: 0.8081 (mp) REVERT: S 17 PHE cc_start: 0.8105 (m-80) cc_final: 0.7900 (m-80) REVERT: S 34 ILE cc_start: 0.8995 (mt) cc_final: 0.8719 (mm) REVERT: T 15 GLU cc_start: 0.7871 (pt0) cc_final: 0.7639 (tp30) REVERT: U 6 LYS cc_start: 0.7531 (mttp) cc_final: 0.7029 (mmmt) REVERT: W 15 ARG cc_start: 0.6961 (mpt90) cc_final: 0.5621 (mtm110) REVERT: Y 45 GLU cc_start: 0.8682 (tp30) cc_final: 0.8441 (tp30) REVERT: Z 15 GLU cc_start: 0.6948 (pp20) cc_final: 0.6614 (pp20) REVERT: 1 9 MET cc_start: 0.5118 (ptp) cc_final: 0.4097 (ttt) REVERT: 1 27 LEU cc_start: 0.9106 (tp) cc_final: 0.8897 (tp) REVERT: 1 37 SER cc_start: 0.8462 (p) cc_final: 0.8261 (p) REVERT: 2 13 THR cc_start: 0.7283 (p) cc_final: 0.6901 (t) REVERT: 2 14 ASP cc_start: 0.6757 (m-30) cc_final: 0.6166 (m-30) REVERT: 7 9 MET cc_start: 0.5746 (mtm) cc_final: 0.4911 (mtt) REVERT: 7 15 ARG cc_start: 0.7773 (mtt-85) cc_final: 0.7478 (tpp-160) REVERT: 7 36 LEU cc_start: 0.7932 (tt) cc_final: 0.7610 (tt) REVERT: 7 42 ASN cc_start: 0.7452 (t0) cc_final: 0.6909 (t0) REVERT: 8 15 GLU cc_start: 0.7339 (tp30) cc_final: 0.6784 (tp30) REVERT: 8 18 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7440 (tm-30) REVERT: 8 25 MET cc_start: 0.8386 (mmt) cc_final: 0.7347 (mmt) REVERT: 8 29 TRP cc_start: 0.7817 (m100) cc_final: 0.7174 (m100) REVERT: 4 9 MET cc_start: 0.6478 (tpt) cc_final: 0.6245 (tpp) REVERT: 4 10 ILE cc_start: 0.7617 (pt) cc_final: 0.7168 (mt) REVERT: 4 34 ILE cc_start: 0.8928 (mt) cc_final: 0.8384 (tp) REVERT: t 15 GLU cc_start: 0.7479 (mp0) cc_final: 0.7184 (mt-10) REVERT: t 18 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7517 (mt0) REVERT: t 24 TYR cc_start: 0.7760 (t80) cc_final: 0.7029 (t80) REVERT: t 29 TRP cc_start: 0.7453 (m100) cc_final: 0.6902 (m100) REVERT: 6 5 TYR cc_start: 0.6043 (p90) cc_final: 0.5435 (p90) REVERT: 5 43 TYR cc_start: 0.7389 (t80) cc_final: 0.6924 (t80) REVERT: C 6 LYS cc_start: 0.7810 (mppt) cc_final: 0.6539 (mmmt) REVERT: C 15 ARG cc_start: 0.5692 (mmm160) cc_final: 0.5307 (mmm160) REVERT: C 35 LEU cc_start: 0.8390 (tp) cc_final: 0.8184 (tp) REVERT: C 43 TRP cc_start: 0.8611 (p90) cc_final: 0.8193 (p90) REVERT: L 139 MET cc_start: 0.4045 (mpp) cc_final: 0.3746 (mpp) REVERT: L 167 PHE cc_start: 0.6234 (t80) cc_final: 0.5731 (t80) REVERT: L 217 ARG cc_start: 0.5010 (mtp180) cc_final: 0.4699 (mtp180) REVERT: M 182 HIS cc_start: 0.6095 (t-90) cc_final: 0.5474 (t-90) REVERT: M 184 ASP cc_start: 0.5688 (t0) cc_final: 0.5159 (m-30) REVERT: M 198 TYR cc_start: 0.3830 (m-10) cc_final: 0.3264 (m-80) REVERT: M 272 MET cc_start: 0.3416 (ttm) cc_final: 0.2562 (tpp) outliers start: 0 outliers final: 0 residues processed: 739 average time/residue: 0.1332 time to fit residues: 158.9652 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 : 0.559 ------------------------------------------------------------------------------- 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: 6.9990 chunk 159 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN 2 21 HIS ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 52 ASN ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 16 GLN ** M 182 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.182408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146800 restraints weight = 41638.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.150385 restraints weight = 54147.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149713 restraints weight = 24802.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.150308 restraints weight = 20125.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.150729 restraints weight = 16519.966| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 23139 Z= 0.260 Angle : 0.860 47.212 32182 Z= 0.403 Chirality : 0.045 0.230 3297 Planarity : 0.005 0.052 3861 Dihedral : 9.277 81.829 3057 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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 aren not related in a simple way. whole: 0.59 (0.17), residues: 2405 helix: 1.30 (0.12), residues: 1561 sheet: 0.21 (1.50), residues: 10 loop : -1.38 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 46 TYR 0.021 0.002 TYR 8 24 PHE 0.032 0.003 PHE Q 11 TRP 0.023 0.002 TRP L 59 HIS 0.010 0.002 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00612 (23119) covalent geometry : angle 0.86049 (32182) hydrogen bonds : bond 0.05227 ( 1286) hydrogen bonds : angle 4.41919 ( 3765) Misc. bond : bond 0.00283 ( 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 726 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 726 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.7010 (ptp90) cc_final: 0.6415 (mtm180) REVERT: D 34 ILE cc_start: 0.8104 (tp) cc_final: 0.7834 (tp) REVERT: E 25 MET cc_start: 0.7114 (mmm) cc_final: 0.6908 (ptt) REVERT: F 15 ARG cc_start: 0.6978 (mmt90) cc_final: 0.6459 (ttm-80) REVERT: G 15 GLU cc_start: 0.7149 (mp0) cc_final: 0.6776 (mp0) REVERT: I 3 LYS cc_start: 0.7642 (mmtp) cc_final: 0.6361 (tptp) REVERT: I 42 ASN cc_start: 0.8419 (t0) cc_final: 0.8080 (t0) REVERT: J 16 GLN cc_start: 0.7110 (mt0) cc_final: 0.6451 (mp10) REVERT: J 29 TRP cc_start: 0.8071 (m100) cc_final: 0.7620 (m-10) REVERT: K 1 MET cc_start: 0.3552 (mmm) cc_final: 0.1731 (ppp) REVERT: N 10 THR cc_start: 0.9065 (p) cc_final: 0.8613 (p) REVERT: Q 7 ILE cc_start: 0.7308 (mm) cc_final: 0.7068 (mm) REVERT: Q 35 LEU cc_start: 0.9250 (mp) cc_final: 0.8995 (mp) REVERT: R 10 THR cc_start: 0.7731 (p) cc_final: 0.7224 (t) REVERT: R 12 LEU cc_start: 0.8569 (mp) cc_final: 0.7961 (mp) REVERT: S 34 ILE cc_start: 0.9084 (mt) cc_final: 0.8782 (mm) REVERT: U 6 LYS cc_start: 0.7577 (mttp) cc_final: 0.7050 (mmtm) REVERT: U 9 MET cc_start: 0.7769 (ppp) cc_final: 0.7470 (ppp) REVERT: W 15 ARG cc_start: 0.7027 (mpt90) cc_final: 0.5920 (ptm-80) REVERT: Y 45 GLU cc_start: 0.8632 (tp30) cc_final: 0.8372 (tp30) REVERT: Z 15 GLU cc_start: 0.7012 (pp20) cc_final: 0.6719 (pp20) REVERT: 1 9 MET cc_start: 0.5095 (ptp) cc_final: 0.4272 (ttt) REVERT: 2 13 THR cc_start: 0.7192 (p) cc_final: 0.6803 (t) REVERT: 2 14 ASP cc_start: 0.6742 (m-30) cc_final: 0.6203 (m-30) REVERT: 2 32 SER cc_start: 0.8922 (m) cc_final: 0.8696 (m) REVERT: 7 9 MET cc_start: 0.5826 (mtm) cc_final: 0.4981 (mtt) REVERT: 7 15 ARG cc_start: 0.8004 (mtt-85) cc_final: 0.7627 (tpp-160) REVERT: 7 36 LEU cc_start: 0.8043 (tt) cc_final: 0.7684 (tt) REVERT: 7 42 ASN cc_start: 0.7488 (t0) cc_final: 0.6944 (t0) REVERT: 8 15 GLU cc_start: 0.7218 (tp30) cc_final: 0.6694 (tp30) REVERT: 8 18 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7396 (tm-30) REVERT: 8 25 MET cc_start: 0.8437 (mmt) cc_final: 0.7703 (mmm) REVERT: 8 29 TRP cc_start: 0.7706 (m100) cc_final: 0.7027 (m100) REVERT: 4 10 ILE cc_start: 0.7611 (pt) cc_final: 0.7092 (mt) REVERT: 4 20 GLN cc_start: 0.7305 (tt0) cc_final: 0.6971 (tt0) REVERT: 4 34 ILE cc_start: 0.8923 (mt) cc_final: 0.8387 (tp) REVERT: t 18 GLN cc_start: 0.7810 (tp-100) cc_final: 0.7599 (tp-100) REVERT: t 24 TYR cc_start: 0.7457 (t80) cc_final: 0.7161 (t80) REVERT: t 29 TRP cc_start: 0.7389 (m100) cc_final: 0.6860 (m100) REVERT: 6 5 TYR cc_start: 0.6010 (p90) cc_final: 0.5448 (p90) REVERT: 5 25 MET cc_start: 0.8527 (mmp) cc_final: 0.8270 (mmp) REVERT: 5 43 TYR cc_start: 0.7310 (t80) cc_final: 0.6812 (t80) REVERT: C 6 LYS cc_start: 0.7825 (mppt) cc_final: 0.6479 (mmmt) REVERT: C 43 TRP cc_start: 0.8634 (p90) cc_final: 0.8194 (p90) REVERT: L 217 ARG cc_start: 0.5175 (mtp180) cc_final: 0.4838 (mtp180) REVERT: M 182 HIS cc_start: 0.5606 (t-90) cc_final: 0.5246 (t-90) REVERT: M 198 TYR cc_start: 0.3845 (m-10) cc_final: 0.3263 (m-80) REVERT: M 272 MET cc_start: 0.3634 (ttm) cc_final: 0.2666 (tpp) outliers start: 0 outliers final: 0 residues processed: 726 average time/residue: 0.1275 time to fit residues: 150.8102 Evaluate side-chains 672 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 672 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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: 20.0000 chunk 152 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 220 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 197 optimal weight: 0.0970 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS 6 52 ASN ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 16 GLN M 193 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.183680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.148083 restraints weight = 40673.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.151102 restraints weight = 46382.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.151374 restraints weight = 23931.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.151162 restraints weight = 20357.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152263 restraints weight = 17074.574| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 23139 Z= 0.163 Angle : 0.765 47.567 32182 Z= 0.356 Chirality : 0.041 0.212 3297 Planarity : 0.004 0.051 3861 Dihedral : 8.993 86.102 3057 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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 aren not related in a simple way. whole: 0.79 (0.17), residues: 2405 helix: 1.46 (0.13), residues: 1569 sheet: 0.10 (1.49), residues: 10 loop : -1.32 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 14 TYR 0.022 0.001 TYR G 24 PHE 0.021 0.002 PHE Y 23 TRP 0.018 0.001 TRP L 262 HIS 0.014 0.001 HIS 0 21 Details of bonding type rmsd covalent geometry : bond 0.00377 (23119) covalent geometry : angle 0.76505 (32182) hydrogen bonds : bond 0.04859 ( 1286) hydrogen bonds : angle 4.24479 ( 3765) Misc. bond : bond 0.00149 ( 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 745 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 745 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6987 (ptp90) cc_final: 0.6390 (mtm180) REVERT: D 34 ILE cc_start: 0.8124 (tp) cc_final: 0.7840 (tp) REVERT: F 45 GLU cc_start: 0.6087 (tp30) cc_final: 0.5851 (tp30) REVERT: G 15 GLU cc_start: 0.7179 (mp0) cc_final: 0.6914 (mp0) REVERT: I 3 LYS cc_start: 0.7721 (mmtp) cc_final: 0.6389 (tptp) REVERT: I 43 TRP cc_start: 0.8392 (p90) cc_final: 0.8043 (p90) REVERT: J 16 GLN cc_start: 0.6964 (mt0) cc_final: 0.6232 (mp10) REVERT: J 29 TRP cc_start: 0.8032 (m100) cc_final: 0.7646 (m-10) REVERT: K 1 MET cc_start: 0.3546 (mmm) cc_final: 0.1663 (ppp) REVERT: N 10 THR cc_start: 0.9071 (p) cc_final: 0.8610 (p) REVERT: O 15 ARG cc_start: 0.5656 (ttp80) cc_final: 0.5343 (ttp80) REVERT: Q 51 TYR cc_start: 0.8342 (m-80) cc_final: 0.8126 (m-10) REVERT: R 10 THR cc_start: 0.7630 (p) cc_final: 0.7132 (t) REVERT: R 12 LEU cc_start: 0.8565 (mp) cc_final: 0.7996 (mp) REVERT: S 34 ILE cc_start: 0.9049 (mt) cc_final: 0.8750 (mm) REVERT: U 6 LYS cc_start: 0.7476 (mttp) cc_final: 0.7058 (mmmt) REVERT: W 15 ARG cc_start: 0.6935 (mpt90) cc_final: 0.5714 (mtm110) REVERT: Y 45 GLU cc_start: 0.8617 (tp30) cc_final: 0.8391 (tp30) REVERT: Z 15 GLU cc_start: 0.6990 (pp20) cc_final: 0.6757 (pp20) REVERT: 1 9 MET cc_start: 0.5021 (ptp) cc_final: 0.4244 (ttt) REVERT: 1 37 SER cc_start: 0.8494 (p) cc_final: 0.8285 (p) REVERT: 2 13 THR cc_start: 0.7162 (p) cc_final: 0.6794 (t) REVERT: 2 14 ASP cc_start: 0.6759 (m-30) cc_final: 0.6225 (m-30) REVERT: 7 9 MET cc_start: 0.5739 (mtm) cc_final: 0.4903 (mtt) REVERT: 7 15 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7632 (tpp-160) REVERT: 7 36 LEU cc_start: 0.8026 (tt) cc_final: 0.7664 (tt) REVERT: 7 42 ASN cc_start: 0.7366 (t0) cc_final: 0.6849 (t0) REVERT: 8 15 GLU cc_start: 0.7190 (tp30) cc_final: 0.6678 (tp30) REVERT: 8 18 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7432 (tm-30) REVERT: 4 10 ILE cc_start: 0.7637 (pt) cc_final: 0.7134 (mt) REVERT: 4 34 ILE cc_start: 0.8911 (mt) cc_final: 0.8347 (tp) REVERT: t 18 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7517 (mt0) REVERT: t 24 TYR cc_start: 0.7707 (t80) cc_final: 0.7178 (t80) REVERT: t 29 TRP cc_start: 0.7418 (m100) cc_final: 0.6888 (m100) REVERT: 6 5 TYR cc_start: 0.5923 (p90) cc_final: 0.5395 (p90) REVERT: 5 25 MET cc_start: 0.8463 (mmp) cc_final: 0.8240 (mmp) REVERT: 5 43 TYR cc_start: 0.7400 (t80) cc_final: 0.6977 (t80) REVERT: C 6 LYS cc_start: 0.7628 (mppt) cc_final: 0.6381 (mmmt) REVERT: C 15 ARG cc_start: 0.5879 (mmm160) cc_final: 0.5421 (mmm160) REVERT: C 43 TRP cc_start: 0.8570 (p90) cc_final: 0.8183 (p90) REVERT: L 206 MET cc_start: 0.1462 (mmp) cc_final: 0.0177 (tpp) REVERT: L 217 ARG cc_start: 0.4991 (mtp180) cc_final: 0.4637 (mtp180) REVERT: M 75 TRP cc_start: 0.4484 (m100) cc_final: 0.4243 (m100) REVERT: M 182 HIS cc_start: 0.5361 (t-90) cc_final: 0.5052 (t-90) REVERT: M 198 TYR cc_start: 0.3972 (m-10) cc_final: 0.3265 (m-80) REVERT: M 272 MET cc_start: 0.3463 (ttm) cc_final: 0.2550 (tpp) REVERT: H 228 LEU cc_start: 0.3930 (tp) cc_final: 0.3355 (pp) outliers start: 0 outliers final: 0 residues processed: 745 average time/residue: 0.1310 time to fit residues: 157.7456 Evaluate side-chains 679 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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: 7.9990 chunk 64 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 184 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN 2 21 HIS ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 52 ASN ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 16 GLN ** M 182 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.181253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.146069 restraints weight = 41628.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148913 restraints weight = 50368.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148981 restraints weight = 25646.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150191 restraints weight = 20629.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.150369 restraints weight = 17385.651| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 23139 Z= 0.247 Angle : 0.849 47.205 32182 Z= 0.398 Chirality : 0.044 0.238 3297 Planarity : 0.005 0.056 3861 Dihedral : 9.249 81.685 3057 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 aren not related in a simple way. whole: 0.49 (0.17), residues: 2405 helix: 1.26 (0.12), residues: 1558 sheet: 0.14 (1.50), residues: 10 loop : -1.47 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 14 TYR 0.025 0.002 TYR G 24 PHE 0.025 0.002 PHE 4 4 TRP 0.020 0.002 TRP L 262 HIS 0.009 0.002 HIS 0 21 Details of bonding type rmsd covalent geometry : bond 0.00586 (23119) covalent geometry : angle 0.84924 (32182) hydrogen bonds : bond 0.05128 ( 1286) hydrogen bonds : angle 4.45502 ( 3765) Misc. bond : bond 0.00261 ( 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 725 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 725 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6834 (ptp90) cc_final: 0.6279 (mtm180) REVERT: D 34 ILE cc_start: 0.8057 (tp) cc_final: 0.7779 (tp) REVERT: G 15 GLU cc_start: 0.7256 (mp0) cc_final: 0.6964 (mp0) REVERT: I 3 LYS cc_start: 0.7643 (mmtp) cc_final: 0.6387 (tptp) REVERT: I 36 LEU cc_start: 0.8674 (mt) cc_final: 0.8461 (mp) REVERT: I 42 ASN cc_start: 0.8350 (t0) cc_final: 0.8062 (t0) REVERT: I 43 TRP cc_start: 0.8452 (p90) cc_final: 0.8169 (p90) REVERT: J 16 GLN cc_start: 0.6930 (mt0) cc_final: 0.6183 (mp10) REVERT: J 29 TRP cc_start: 0.8071 (m100) cc_final: 0.7645 (m-10) REVERT: K 1 MET cc_start: 0.3518 (mmm) cc_final: 0.1781 (ppp) REVERT: N 10 THR cc_start: 0.9046 (p) cc_final: 0.8597 (p) REVERT: Q 51 TYR cc_start: 0.8324 (m-80) cc_final: 0.7971 (m-10) REVERT: R 10 THR cc_start: 0.7660 (p) cc_final: 0.7192 (t) REVERT: R 12 LEU cc_start: 0.8530 (mp) cc_final: 0.7937 (mp) REVERT: S 34 ILE cc_start: 0.9084 (mt) cc_final: 0.8786 (mm) REVERT: U 6 LYS cc_start: 0.7665 (mttp) cc_final: 0.6991 (mmtm) REVERT: W 15 ARG cc_start: 0.6949 (mpt90) cc_final: 0.5795 (mtm110) REVERT: Y 45 GLU cc_start: 0.8615 (tp30) cc_final: 0.8380 (tp30) REVERT: Z 15 GLU cc_start: 0.7035 (pp20) cc_final: 0.6767 (pp20) REVERT: 1 9 MET cc_start: 0.5226 (ptp) cc_final: 0.4389 (ttt) REVERT: 1 27 LEU cc_start: 0.9104 (tp) cc_final: 0.8892 (tp) REVERT: 1 37 SER cc_start: 0.8479 (p) cc_final: 0.8275 (p) REVERT: 2 13 THR cc_start: 0.7235 (p) cc_final: 0.6842 (t) REVERT: 2 14 ASP cc_start: 0.6696 (m-30) cc_final: 0.6170 (m-30) REVERT: 2 32 SER cc_start: 0.8891 (m) cc_final: 0.8679 (m) REVERT: 7 9 MET cc_start: 0.5815 (mtm) cc_final: 0.4953 (mtt) REVERT: 7 15 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7557 (tpp-160) REVERT: 7 36 LEU cc_start: 0.8035 (tt) cc_final: 0.7666 (tt) REVERT: 7 42 ASN cc_start: 0.7478 (t0) cc_final: 0.6960 (t0) REVERT: 8 15 GLU cc_start: 0.7200 (tp30) cc_final: 0.6705 (tp30) REVERT: 8 18 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7422 (tm-30) REVERT: 8 21 HIS cc_start: 0.8175 (t-170) cc_final: 0.7931 (t-170) REVERT: 8 25 MET cc_start: 0.8448 (mmm) cc_final: 0.7699 (mmt) REVERT: 8 29 TRP cc_start: 0.7635 (m100) cc_final: 0.6955 (m100) REVERT: 4 9 MET cc_start: 0.6725 (tpp) cc_final: 0.6345 (tpt) REVERT: 4 10 ILE cc_start: 0.7481 (pt) cc_final: 0.7108 (mt) REVERT: 4 20 GLN cc_start: 0.7295 (tt0) cc_final: 0.6940 (tt0) REVERT: 4 34 ILE cc_start: 0.8949 (mt) cc_final: 0.8386 (tp) REVERT: t 24 TYR cc_start: 0.7625 (t80) cc_final: 0.6939 (t80) REVERT: t 29 TRP cc_start: 0.7397 (m100) cc_final: 0.6845 (m100) REVERT: 6 5 TYR cc_start: 0.5960 (p90) cc_final: 0.5406 (p90) REVERT: 5 25 MET cc_start: 0.8490 (mmp) cc_final: 0.8229 (mmp) REVERT: 5 43 TYR cc_start: 0.7336 (t80) cc_final: 0.6859 (t80) REVERT: C 6 LYS cc_start: 0.7764 (mppt) cc_final: 0.6436 (mmmt) REVERT: C 43 TRP cc_start: 0.8594 (p90) cc_final: 0.8172 (p90) REVERT: L 139 MET cc_start: 0.4286 (mpp) cc_final: 0.3999 (mpp) REVERT: L 206 MET cc_start: 0.1188 (mmp) cc_final: -0.0092 (tpp) REVERT: L 217 ARG cc_start: 0.5181 (mtp180) cc_final: 0.4830 (mtp180) REVERT: M 75 TRP cc_start: 0.4384 (m100) cc_final: 0.3869 (m-10) REVERT: M 182 HIS cc_start: 0.5495 (t-90) cc_final: 0.5163 (t-90) REVERT: M 198 TYR cc_start: 0.3788 (m-10) cc_final: 0.3192 (m-80) REVERT: M 272 MET cc_start: 0.3208 (ttm) cc_final: 0.2323 (tpp) REVERT: H 128 HIS cc_start: 0.5906 (m-70) cc_final: 0.5530 (t-90) outliers start: 0 outliers final: 0 residues processed: 725 average time/residue: 0.1310 time to fit residues: 154.3981 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 : 0.709 ------------------------------------------------------------------------------- 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: 3.9990 chunk 50 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 209 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN t 18 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.183859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.151372 restraints weight = 40372.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154451 restraints weight = 49652.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154393 restraints weight = 24962.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.154612 restraints weight = 18557.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.155193 restraints weight = 16158.390| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 23139 Z= 0.134 Angle : 0.744 47.806 32182 Z= 0.347 Chirality : 0.040 0.222 3297 Planarity : 0.004 0.054 3861 Dihedral : 8.921 88.952 3057 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 aren not related in a simple way. whole: 0.82 (0.17), residues: 2405 helix: 1.55 (0.13), residues: 1573 sheet: 0.05 (1.51), residues: 10 loop : -1.48 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 14 TYR 0.019 0.001 TYR 8 24 PHE 0.034 0.001 PHE S 17 TRP 0.050 0.001 TRP J 45 HIS 0.008 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00303 (23119) covalent geometry : angle 0.74422 (32182) hydrogen bonds : bond 0.04718 ( 1286) hydrogen bonds : angle 4.19836 ( 3765) Misc. bond : bond 0.00085 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3717.42 seconds wall clock time: 64 minutes 58.85 seconds (3898.85 seconds total)