Starting phenix.real_space_refine on Tue Aug 26 01:53:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m54_30084/08_2025/6m54_30084.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m54_30084/08_2025/6m54_30084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m54_30084/08_2025/6m54_30084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m54_30084/08_2025/6m54_30084.map" model { file = "/net/cci-nas-00/data/ceres_data/6m54_30084/08_2025/6m54_30084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m54_30084/08_2025/6m54_30084.cif" } resolution = 2.4 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= 0.008 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: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 168 5.16 5 C 20978 2.51 5 N 5886 2.21 5 O 6344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33382 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "B" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "D" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "E" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "G" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "H" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "J" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "M" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "N" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "O" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "Q" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "R" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "S" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "T" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 11.97, per 1000 atoms: 0.36 Number of scatterers: 33382 At special positions: 0 Unit cell: (136.59, 136.59, 136.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 6 26.01 S 168 16.00 O 6344 8.00 N 5886 7.00 C 20978 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=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 238.4 nanoseconds 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7892 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 14 through 42 removed outlier: 3.765A pdb=" N ASN A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 42 " --> pdb=" O MET A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 78 removed outlier: 3.571A pdb=" N ARG A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 125 removed outlier: 3.640A pdb=" N ASN A 110 " --> pdb=" O HIS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 138 through 160 removed outlier: 3.509A pdb=" N GLN A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.903A pdb=" N GLU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 42 " --> pdb=" O MET B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 78 removed outlier: 3.723A pdb=" N ARG B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 125 removed outlier: 3.556A pdb=" N ALA B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B 110 " --> pdb=" O HIS B 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 138 through 160 removed outlier: 3.647A pdb=" N GLN B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.936A pdb=" N GLU B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 42 removed outlier: 3.689A pdb=" N ASN C 26 " --> pdb=" O ASN C 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 78 removed outlier: 3.684A pdb=" N ARG C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 65 " --> pdb=" O HIS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 125 removed outlier: 3.617A pdb=" N ASN C 110 " --> pdb=" O HIS C 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 138 through 160 removed outlier: 3.669A pdb=" N GLN C 142 " --> pdb=" O TYR C 138 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 175 removed outlier: 3.917A pdb=" N GLU C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 78 removed outlier: 3.685A pdb=" N ARG D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 65 " --> pdb=" O HIS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 removed outlier: 3.562A pdb=" N ALA D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 138 through 160 removed outlier: 3.667A pdb=" N GLN D 142 " --> pdb=" O TYR D 138 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 175 removed outlier: 3.900A pdb=" N GLU D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE E 42 " --> pdb=" O MET E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 78 removed outlier: 3.720A pdb=" N ARG E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU E 65 " --> pdb=" O HIS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 125 removed outlier: 3.558A pdb=" N ALA E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET E 101 " --> pdb=" O GLY E 97 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN E 110 " --> pdb=" O HIS E 106 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 138 Processing helix chain 'E' and resid 138 through 160 removed outlier: 3.644A pdb=" N GLN E 142 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 175 removed outlier: 3.936A pdb=" N GLU E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 42 removed outlier: 3.689A pdb=" N ASN F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE F 42 " --> pdb=" O MET F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 78 removed outlier: 3.683A pdb=" N ARG F 64 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 125 removed outlier: 3.618A pdb=" N ASN F 110 " --> pdb=" O HIS F 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 138 Processing helix chain 'F' and resid 138 through 160 removed outlier: 3.669A pdb=" N GLN F 142 " --> pdb=" O TYR F 138 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 175 removed outlier: 3.907A pdb=" N GLU F 168 " --> pdb=" O SER F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 42 removed outlier: 3.689A pdb=" N ASN G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 78 removed outlier: 3.684A pdb=" N ARG G 64 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU G 65 " --> pdb=" O HIS G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 125 removed outlier: 3.563A pdb=" N ALA G 100 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET G 101 " --> pdb=" O GLY G 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN G 110 " --> pdb=" O HIS G 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 138 Processing helix chain 'G' and resid 138 through 160 removed outlier: 3.668A pdb=" N GLN G 142 " --> pdb=" O TYR G 138 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 175 removed outlier: 3.916A pdb=" N GLU G 168 " --> pdb=" O SER G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 42 removed outlier: 3.689A pdb=" N ASN H 26 " --> pdb=" O ASN H 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE H 42 " --> pdb=" O MET H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 78 removed outlier: 3.704A pdb=" N ARG H 64 " --> pdb=" O SER H 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU H 65 " --> pdb=" O HIS H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 125 removed outlier: 3.555A pdb=" N ALA H 100 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET H 101 " --> pdb=" O GLY H 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN H 110 " --> pdb=" O HIS H 106 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU H 117 " --> pdb=" O GLN H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 138 Processing helix chain 'H' and resid 138 through 160 removed outlier: 3.644A pdb=" N GLN H 142 " --> pdb=" O TYR H 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY H 160 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 175 removed outlier: 3.935A pdb=" N GLU H 168 " --> pdb=" O SER H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN I 26 " --> pdb=" O ASN I 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE I 42 " --> pdb=" O MET I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 78 removed outlier: 3.683A pdb=" N ARG I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU I 65 " --> pdb=" O HIS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 125 removed outlier: 3.555A pdb=" N ALA I 100 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET I 101 " --> pdb=" O GLY I 97 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN I 110 " --> pdb=" O HIS I 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU I 117 " --> pdb=" O GLN I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 138 Processing helix chain 'I' and resid 138 through 160 removed outlier: 3.667A pdb=" N GLN I 142 " --> pdb=" O TYR I 138 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL I 143 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY I 160 " --> pdb=" O LEU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 175 removed outlier: 3.916A pdb=" N GLU I 168 " --> pdb=" O SER I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN J 26 " --> pdb=" O ASN J 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE J 42 " --> pdb=" O MET J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 78 removed outlier: 3.720A pdb=" N ARG J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU J 65 " --> pdb=" O HIS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.556A pdb=" N ALA J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET J 101 " --> pdb=" O GLY J 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN J 110 " --> pdb=" O HIS J 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 138 Processing helix chain 'J' and resid 138 through 160 removed outlier: 3.643A pdb=" N GLN J 142 " --> pdb=" O TYR J 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY J 160 " --> pdb=" O LEU J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 175 removed outlier: 3.936A pdb=" N GLU J 168 " --> pdb=" O SER J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN K 26 " --> pdb=" O ASN K 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE K 42 " --> pdb=" O MET K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 78 removed outlier: 3.704A pdb=" N ARG K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU K 65 " --> pdb=" O HIS K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 125 removed outlier: 3.555A pdb=" N ALA K 100 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET K 101 " --> pdb=" O GLY K 97 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN K 110 " --> pdb=" O HIS K 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU K 117 " --> pdb=" O GLN K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 138 Processing helix chain 'K' and resid 138 through 160 removed outlier: 3.644A pdb=" N GLN K 142 " --> pdb=" O TYR K 138 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL K 143 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY K 160 " --> pdb=" O LEU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 175 removed outlier: 3.935A pdb=" N GLU K 168 " --> pdb=" O SER K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN L 26 " --> pdb=" O ASN L 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE L 42 " --> pdb=" O MET L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 78 removed outlier: 3.683A pdb=" N ARG L 64 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU L 65 " --> pdb=" O HIS L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 125 removed outlier: 3.562A pdb=" N ALA L 100 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET L 101 " --> pdb=" O GLY L 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN L 110 " --> pdb=" O HIS L 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU L 117 " --> pdb=" O GLN L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 138 Processing helix chain 'L' and resid 138 through 160 removed outlier: 3.669A pdb=" N GLN L 142 " --> pdb=" O TYR L 138 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 175 removed outlier: 3.915A pdb=" N GLU L 168 " --> pdb=" O SER L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 42 removed outlier: 3.689A pdb=" N ASN M 26 " --> pdb=" O ASN M 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE M 42 " --> pdb=" O MET M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 78 removed outlier: 3.683A pdb=" N ARG M 64 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU M 65 " --> pdb=" O HIS M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 125 removed outlier: 3.555A pdb=" N ALA M 100 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET M 101 " --> pdb=" O GLY M 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN M 110 " --> pdb=" O HIS M 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU M 117 " --> pdb=" O GLN M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 138 Processing helix chain 'M' and resid 138 through 160 removed outlier: 3.667A pdb=" N GLN M 142 " --> pdb=" O TYR M 138 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL M 143 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY M 160 " --> pdb=" O LEU M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 175 removed outlier: 3.916A pdb=" N GLU M 168 " --> pdb=" O SER M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 42 removed outlier: 3.689A pdb=" N ASN N 26 " --> pdb=" O ASN N 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE N 42 " --> pdb=" O MET N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 78 removed outlier: 3.683A pdb=" N ARG N 64 " --> pdb=" O SER N 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU N 65 " --> pdb=" O HIS N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 125 removed outlier: 3.563A pdb=" N ALA N 100 " --> pdb=" O SER N 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET N 101 " --> pdb=" O GLY N 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN N 110 " --> pdb=" O HIS N 106 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU N 117 " --> pdb=" O GLN N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 138 Processing helix chain 'N' and resid 138 through 160 removed outlier: 3.669A pdb=" N GLN N 142 " --> pdb=" O TYR N 138 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL N 143 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY N 160 " --> pdb=" O LEU N 156 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 175 removed outlier: 3.917A pdb=" N GLU N 168 " --> pdb=" O SER N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN O 26 " --> pdb=" O ASN O 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE O 42 " --> pdb=" O MET O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 78 removed outlier: 3.721A pdb=" N ARG O 64 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU O 65 " --> pdb=" O HIS O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 125 removed outlier: 3.557A pdb=" N ALA O 100 " --> pdb=" O SER O 96 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET O 101 " --> pdb=" O GLY O 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN O 110 " --> pdb=" O HIS O 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 138 Processing helix chain 'O' and resid 138 through 160 removed outlier: 3.662A pdb=" N GLN O 142 " --> pdb=" O TYR O 138 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL O 143 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 175 removed outlier: 3.935A pdb=" N GLU O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN P 26 " --> pdb=" O ASN P 22 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE P 42 " --> pdb=" O MET P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 78 removed outlier: 3.721A pdb=" N ARG P 64 " --> pdb=" O SER P 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU P 65 " --> pdb=" O HIS P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 125 removed outlier: 3.567A pdb=" N ALA P 100 " --> pdb=" O SER P 96 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET P 101 " --> pdb=" O GLY P 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN P 110 " --> pdb=" O HIS P 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 138 Processing helix chain 'P' and resid 138 through 160 removed outlier: 3.644A pdb=" N GLN P 142 " --> pdb=" O TYR P 138 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL P 143 " --> pdb=" O LEU P 139 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY P 160 " --> pdb=" O LEU P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 175 removed outlier: 3.934A pdb=" N GLU P 168 " --> pdb=" O SER P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 42 removed outlier: 3.689A pdb=" N ASN Q 26 " --> pdb=" O ASN Q 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 78 removed outlier: 3.683A pdb=" N ARG Q 64 " --> pdb=" O SER Q 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU Q 65 " --> pdb=" O HIS Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 125 removed outlier: 3.561A pdb=" N ALA Q 100 " --> pdb=" O SER Q 96 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET Q 101 " --> pdb=" O GLY Q 97 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN Q 110 " --> pdb=" O HIS Q 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 138 Processing helix chain 'Q' and resid 138 through 160 removed outlier: 3.668A pdb=" N GLN Q 142 " --> pdb=" O TYR Q 138 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY Q 160 " --> pdb=" O LEU Q 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 175 removed outlier: 3.912A pdb=" N GLU Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN R 26 " --> pdb=" O ASN R 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE R 42 " --> pdb=" O MET R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 78 removed outlier: 3.704A pdb=" N ARG R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU R 65 " --> pdb=" O HIS R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 125 removed outlier: 3.557A pdb=" N ALA R 100 " --> pdb=" O SER R 96 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET R 101 " --> pdb=" O GLY R 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN R 110 " --> pdb=" O HIS R 106 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU R 117 " --> pdb=" O GLN R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 138 Processing helix chain 'R' and resid 138 through 160 removed outlier: 3.644A pdb=" N GLN R 142 " --> pdb=" O TYR R 138 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL R 143 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 175 removed outlier: 3.934A pdb=" N GLU R 168 " --> pdb=" O SER R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN S 26 " --> pdb=" O ASN S 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE S 42 " --> pdb=" O MET S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 78 removed outlier: 3.722A pdb=" N ARG S 64 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU S 65 " --> pdb=" O HIS S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 125 removed outlier: 3.555A pdb=" N ALA S 100 " --> pdb=" O SER S 96 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN S 110 " --> pdb=" O HIS S 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU S 117 " --> pdb=" O GLN S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 138 Processing helix chain 'S' and resid 138 through 160 removed outlier: 3.646A pdb=" N GLN S 142 " --> pdb=" O TYR S 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL S 143 " --> pdb=" O LEU S 139 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY S 160 " --> pdb=" O LEU S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 164 through 175 removed outlier: 3.935A pdb=" N GLU S 168 " --> pdb=" O SER S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN T 26 " --> pdb=" O ASN T 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR T 40 " --> pdb=" O LEU T 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE T 42 " --> pdb=" O MET T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 78 removed outlier: 3.704A pdb=" N ARG T 64 " --> pdb=" O SER T 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU T 65 " --> pdb=" O HIS T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 125 removed outlier: 3.556A pdb=" N ALA T 100 " --> pdb=" O SER T 96 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET T 101 " --> pdb=" O GLY T 97 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN T 110 " --> pdb=" O HIS T 106 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU T 117 " --> pdb=" O GLN T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 138 Processing helix chain 'T' and resid 138 through 160 removed outlier: 3.647A pdb=" N GLN T 142 " --> pdb=" O TYR T 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL T 143 " --> pdb=" O LEU T 139 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY T 160 " --> pdb=" O LEU T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 175 removed outlier: 3.935A pdb=" N GLU T 168 " --> pdb=" O SER T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN U 26 " --> pdb=" O ASN U 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE U 42 " --> pdb=" O MET U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 78 removed outlier: 3.721A pdb=" N ARG U 64 " --> pdb=" O SER U 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 125 removed outlier: 3.550A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN U 110 " --> pdb=" O HIS U 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU U 117 " --> pdb=" O GLN U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 138 Processing helix chain 'U' and resid 138 through 160 removed outlier: 3.647A pdb=" N GLN U 142 " --> pdb=" O TYR U 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL U 143 " --> pdb=" O LEU U 139 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY U 160 " --> pdb=" O LEU U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 175 removed outlier: 3.935A pdb=" N GLU U 168 " --> pdb=" O SER U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 42 removed outlier: 3.689A pdb=" N ASN V 26 " --> pdb=" O ASN V 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR V 40 " --> pdb=" O LEU V 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE V 42 " --> pdb=" O MET V 38 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 78 removed outlier: 3.725A pdb=" N ARG V 64 " --> pdb=" O SER V 60 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 125 removed outlier: 3.524A pdb=" N ALA V 100 " --> pdb=" O SER V 96 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN V 110 " --> pdb=" O HIS V 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU V 117 " --> pdb=" O GLN V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 138 Processing helix chain 'V' and resid 138 through 160 removed outlier: 3.644A pdb=" N GLN V 142 " --> pdb=" O TYR V 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL V 143 " --> pdb=" O LEU V 139 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY V 160 " --> pdb=" O LEU V 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 164 through 175 removed outlier: 3.935A pdb=" N GLU V 168 " --> pdb=" O SER V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN W 26 " --> pdb=" O ASN W 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR W 40 " --> pdb=" O LEU W 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE W 42 " --> pdb=" O MET W 38 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 78 removed outlier: 3.722A pdb=" N ARG W 64 " --> pdb=" O SER W 60 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU W 65 " --> pdb=" O HIS W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 125 removed outlier: 3.615A pdb=" N ASN W 110 " --> pdb=" O HIS W 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU W 117 " --> pdb=" O GLN W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 138 Processing helix chain 'W' and resid 138 through 160 removed outlier: 3.648A pdb=" N GLN W 142 " --> pdb=" O TYR W 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY W 160 " --> pdb=" O LEU W 156 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 175 removed outlier: 3.935A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 42 removed outlier: 3.690A pdb=" N ASN X 26 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR X 40 " --> pdb=" O LEU X 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE X 42 " --> pdb=" O MET X 38 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 78 removed outlier: 3.704A pdb=" N ARG X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU X 65 " --> pdb=" O HIS X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 125 removed outlier: 3.615A pdb=" N ASN X 110 " --> pdb=" O HIS X 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU X 117 " --> pdb=" O GLN X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 138 Processing helix chain 'X' and resid 138 through 160 removed outlier: 3.647A pdb=" N GLN X 142 " --> pdb=" O TYR X 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL X 143 " --> pdb=" O LEU X 139 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY X 160 " --> pdb=" O LEU X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 175 removed outlier: 3.935A pdb=" N GLU X 168 " --> pdb=" O SER X 164 " (cutoff:3.500A) 2391 hydrogen bonds defined for protein. 7173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.75 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7349 1.33 - 1.44: 7729 1.44 - 1.56: 18732 1.56 - 1.68: 0 1.68 - 1.80: 264 Bond restraints: 34074 Sorted by residual: bond pdb=" CB LYS X 69 " pdb=" CG LYS X 69 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.97e+00 bond pdb=" CB LYS B 69 " pdb=" CG LYS B 69 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.90e+00 bond pdb=" CB LYS W 69 " pdb=" CG LYS W 69 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.88e+00 bond pdb=" CB LYS O 69 " pdb=" CG LYS O 69 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.88e+00 bond pdb=" CB LYS R 69 " pdb=" CG LYS R 69 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.86e+00 ... (remaining 34069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 43049 2.11 - 4.22: 2579 4.22 - 6.33: 298 6.33 - 8.44: 22 8.44 - 10.55: 22 Bond angle restraints: 45970 Sorted by residual: angle pdb=" N GLU X 95 " pdb=" CA GLU X 95 " pdb=" C GLU X 95 " ideal model delta sigma weight residual 110.80 121.35 -10.55 2.13e+00 2.20e-01 2.45e+01 angle pdb=" N GLU W 95 " pdb=" CA GLU W 95 " pdb=" C GLU W 95 " ideal model delta sigma weight residual 110.80 121.33 -10.53 2.13e+00 2.20e-01 2.44e+01 angle pdb=" N GLU C 95 " pdb=" CA GLU C 95 " pdb=" C GLU C 95 " ideal model delta sigma weight residual 110.80 121.30 -10.50 2.13e+00 2.20e-01 2.43e+01 angle pdb=" N GLU F 95 " pdb=" CA GLU F 95 " pdb=" C GLU F 95 " ideal model delta sigma weight residual 110.80 121.09 -10.29 2.13e+00 2.20e-01 2.34e+01 angle pdb=" C HIS A 137 " pdb=" N TYR A 138 " pdb=" CA TYR A 138 " ideal model delta sigma weight residual 122.42 114.63 7.79 1.77e+00 3.19e-01 1.93e+01 ... (remaining 45965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 18144 16.46 - 32.92: 1794 32.92 - 49.38: 519 49.38 - 65.84: 57 65.84 - 82.30: 48 Dihedral angle restraints: 20562 sinusoidal: 8354 harmonic: 12208 Sorted by residual: dihedral pdb=" CA TYR G 138 " pdb=" C TYR G 138 " pdb=" N LEU G 139 " pdb=" CA LEU G 139 " ideal model delta harmonic sigma weight residual -180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA TYR I 138 " pdb=" C TYR I 138 " pdb=" N LEU I 139 " pdb=" CA LEU I 139 " ideal model delta harmonic sigma weight residual -180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA TYR M 138 " pdb=" C TYR M 138 " pdb=" N LEU M 139 " pdb=" CA LEU M 139 " ideal model delta harmonic sigma weight residual -180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 20559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2104 0.047 - 0.094: 1865 0.094 - 0.142: 654 0.142 - 0.189: 186 0.189 - 0.236: 49 Chirality restraints: 4858 Sorted by residual: chirality pdb=" CG LEU A 73 " pdb=" CB LEU A 73 " pdb=" CD1 LEU A 73 " pdb=" CD2 LEU A 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CG LEU L 73 " pdb=" CB LEU L 73 " pdb=" CD1 LEU L 73 " pdb=" CD2 LEU L 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU N 73 " pdb=" CB LEU N 73 " pdb=" CD1 LEU N 73 " pdb=" CD2 LEU N 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4855 not shown) Planarity restraints: 6068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 33 " 0.034 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR B 33 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR B 33 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 33 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 33 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 33 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 33 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 33 " 0.034 2.00e-02 2.50e+03 2.80e-02 1.57e+01 pdb=" CG TYR S 33 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR S 33 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR S 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR S 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR S 33 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR S 33 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR S 33 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 33 " -0.034 2.00e-02 2.50e+03 2.80e-02 1.57e+01 pdb=" CG TYR E 33 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR E 33 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR E 33 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR E 33 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 33 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 33 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR E 33 " -0.003 2.00e-02 2.50e+03 ... (remaining 6065 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 18513 3.05 - 3.51: 31104 3.51 - 3.98: 51659 3.98 - 4.44: 63207 4.44 - 4.90: 92785 Nonbonded interactions: 257268 Sorted by model distance: nonbonded pdb=" O HIS A 137 " pdb=" CA TYR A 138 " model vdw 2.591 2.776 nonbonded pdb=" N SER W 96 " pdb=" O SER W 96 " model vdw 2.611 2.496 nonbonded pdb=" N SER X 96 " pdb=" O SER X 96 " model vdw 2.612 2.496 nonbonded pdb=" N SER C 96 " pdb=" O SER C 96 " model vdw 2.613 2.496 nonbonded pdb=" N ASP U 46 " pdb=" OD1 ASP U 46 " model vdw 2.615 3.120 ... (remaining 257263 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 'A' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'B' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'C' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'D' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'E' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'F' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'G' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'H' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'I' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'J' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'K' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'L' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'M' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'N' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'O' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'P' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'Q' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'R' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'S' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'T' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'U' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'V' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'W' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'X' and (resid 6 through 63 or resid 65 through 176)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.990 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.100 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.012 0.070 34074 Z= 0.526 Angle : 1.145 10.547 45970 Z= 0.685 Chirality : 0.071 0.236 4858 Planarity : 0.006 0.054 6068 Dihedral : 14.960 82.302 12670 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.37 (0.11), residues: 4066 helix: 0.43 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -2.30 (0.14), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 10 TYR 0.068 0.006 TYR B 33 PHE 0.018 0.006 PHE A 56 TRP 0.007 0.002 TRP L 94 HIS 0.005 0.002 HIS R 66 Details of bonding type rmsd covalent geometry : bond 0.01183 (34074) covalent geometry : angle 1.14512 (45970) hydrogen bonds : bond 0.23223 ( 2391) hydrogen bonds : angle 5.04580 ( 7173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 1.423 Fit side-chains REVERT: A 120 LYS cc_start: 0.7896 (tttm) cc_final: 0.7538 (ttmp) REVERT: B 64 ARG cc_start: 0.7217 (tpt-90) cc_final: 0.6233 (ttm170) REVERT: F 120 LYS cc_start: 0.8052 (tttm) cc_final: 0.7695 (ttmp) REVERT: H 64 ARG cc_start: 0.7294 (tpt-90) cc_final: 0.6278 (ttm170) REVERT: I 120 LYS cc_start: 0.7934 (tttm) cc_final: 0.7573 (ttmp) REVERT: L 120 LYS cc_start: 0.7874 (tttm) cc_final: 0.7509 (ttmp) REVERT: M 120 LYS cc_start: 0.7986 (tttm) cc_final: 0.7619 (ttmp) REVERT: Q 120 LYS cc_start: 0.7871 (tttm) cc_final: 0.7504 (ttmp) REVERT: V 95 GLU cc_start: 0.7420 (pt0) cc_final: 0.7096 (pt0) outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 1.2118 time to fit residues: 650.9357 Evaluate side-chains 397 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 15 GLN A 51 ASN A 110 ASN B 14 HIS B 15 GLN B 51 ASN B 110 ASN B 113 GLN C 14 HIS C 15 GLN C 51 ASN C 110 ASN C 113 GLN D 14 HIS D 15 GLN D 51 ASN D 110 ASN D 113 GLN E 14 HIS E 15 GLN E 51 ASN E 110 ASN E 113 GLN F 14 HIS F 15 GLN F 51 ASN F 110 ASN F 113 GLN G 14 HIS G 15 GLN G 51 ASN G 110 ASN G 113 GLN H 14 HIS H 15 GLN H 51 ASN H 110 ASN H 113 GLN I 14 HIS I 15 GLN I 51 ASN I 110 ASN I 113 GLN J 14 HIS J 15 GLN J 51 ASN J 110 ASN J 113 GLN K 14 HIS K 15 GLN K 51 ASN K 110 ASN K 113 GLN L 14 HIS L 15 GLN L 51 ASN L 110 ASN L 113 GLN M 14 HIS M 15 GLN M 51 ASN M 110 ASN M 113 GLN N 14 HIS N 15 GLN N 51 ASN N 110 ASN N 113 GLN O 14 HIS O 15 GLN O 51 ASN O 110 ASN O 113 GLN P 14 HIS P 15 GLN P 51 ASN P 110 ASN P 113 GLN Q 14 HIS Q 15 GLN Q 51 ASN Q 110 ASN Q 113 GLN R 14 HIS R 15 GLN R 51 ASN R 110 ASN R 113 GLN S 14 HIS S 15 GLN S 51 ASN S 110 ASN S 113 GLN T 14 HIS T 15 GLN T 51 ASN T 110 ASN T 113 GLN U 14 HIS U 15 GLN U 51 ASN U 110 ASN U 113 GLN V 14 HIS V 15 GLN V 51 ASN V 110 ASN V 113 GLN W 14 HIS W 15 GLN W 51 ASN W 110 ASN W 113 GLN X 14 HIS X 15 GLN X 51 ASN X 110 ASN X 113 GLN Total number of N/Q/H flips: 119 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108474 restraints weight = 82860.389| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.65 r_work: 0.3139 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34074 Z= 0.186 Angle : 0.553 5.552 45970 Z= 0.320 Chirality : 0.039 0.131 4858 Planarity : 0.003 0.025 6068 Dihedral : 4.277 22.140 4494 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.06 % Allowed : 5.06 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.11 (0.12), residues: 4066 helix: 3.03 (0.08), residues: 3130 sheet: None (None), residues: 0 loop : -1.59 (0.15), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 157 TYR 0.018 0.002 TYR B 33 PHE 0.006 0.001 PHE A 52 TRP 0.011 0.002 TRP I 94 HIS 0.002 0.001 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00286 (34074) covalent geometry : angle 0.55254 (45970) hydrogen bonds : bond 0.10271 ( 2391) hydrogen bonds : angle 3.71640 ( 7173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 439 time to evaluate : 1.457 Fit side-chains REVERT: A 120 LYS cc_start: 0.8591 (tttm) cc_final: 0.8390 (ttmp) REVERT: B 64 ARG cc_start: 0.8082 (tpt-90) cc_final: 0.7748 (ttm170) REVERT: H 64 ARG cc_start: 0.8166 (tpt-90) cc_final: 0.7783 (ttm170) REVERT: L 120 LYS cc_start: 0.8657 (tttm) cc_final: 0.8456 (ttmp) outliers start: 2 outliers final: 0 residues processed: 441 average time/residue: 1.1853 time to fit residues: 584.2716 Evaluate side-chains 371 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 26 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 395 optimal weight: 5.9990 chunk 366 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 399 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 352 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 113 GLN C 113 GLN D 113 GLN E 113 GLN E 140 ASN G 113 GLN H 113 GLN H 140 ASN I 113 GLN J 113 GLN J 140 ASN K 113 GLN K 140 ASN L 113 GLN M 113 GLN N 113 GLN O 113 GLN P 113 GLN P 140 ASN Q 113 GLN R 113 GLN R 140 ASN S 113 GLN T 113 GLN U 113 GLN V 113 GLN V 140 ASN W 113 GLN X 113 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.098899 restraints weight = 85221.192| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.75 r_work: 0.2992 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 34074 Z= 0.248 Angle : 0.638 6.679 45970 Z= 0.370 Chirality : 0.043 0.137 4858 Planarity : 0.004 0.025 6068 Dihedral : 4.458 22.733 4494 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.55 % Allowed : 7.97 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.36 (0.12), residues: 4066 helix: 3.19 (0.08), residues: 3130 sheet: None (None), residues: 0 loop : -1.42 (0.15), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 77 TYR 0.019 0.002 TYR H 33 PHE 0.009 0.002 PHE A 56 TRP 0.006 0.001 TRP N 94 HIS 0.002 0.001 HIS M 14 Details of bonding type rmsd covalent geometry : bond 0.00425 (34074) covalent geometry : angle 0.63812 (45970) hydrogen bonds : bond 0.13536 ( 2391) hydrogen bonds : angle 4.00426 ( 7173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 379 time to evaluate : 1.262 Fit side-chains REVERT: A 120 LYS cc_start: 0.8697 (tttm) cc_final: 0.8475 (ttmp) REVERT: B 64 ARG cc_start: 0.8215 (tpt-90) cc_final: 0.7737 (ttm170) REVERT: H 64 ARG cc_start: 0.8275 (tpt-90) cc_final: 0.7795 (ttm170) REVERT: L 120 LYS cc_start: 0.8749 (tttm) cc_final: 0.8540 (tttp) outliers start: 55 outliers final: 35 residues processed: 393 average time/residue: 1.0401 time to fit residues: 460.6531 Evaluate side-chains 399 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 364 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain N residue 159 MET Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 159 MET Chi-restraints excluded: chain P residue 159 MET Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain U residue 159 MET Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain V residue 159 MET Chi-restraints excluded: chain W residue 159 MET Chi-restraints excluded: chain X residue 159 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 318 optimal weight: 5.9990 chunk 361 optimal weight: 5.9990 chunk 266 optimal weight: 7.9990 chunk 306 optimal weight: 0.0570 chunk 252 optimal weight: 7.9990 chunk 278 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 311 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 113 GLN B 113 GLN D 140 ASN E 113 GLN F 113 GLN H 113 GLN J 113 GLN K 113 GLN O 113 GLN P 113 GLN R 113 GLN S 113 GLN T 113 GLN U 113 GLN V 113 GLN W 113 GLN X 113 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102143 restraints weight = 77894.788| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.67 r_work: 0.3044 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 34074 Z= 0.215 Angle : 0.580 6.063 45970 Z= 0.336 Chirality : 0.041 0.128 4858 Planarity : 0.003 0.020 6068 Dihedral : 4.301 22.616 4494 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.27 % Allowed : 9.84 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.80 (0.12), residues: 4066 helix: 3.50 (0.08), residues: 3130 sheet: None (None), residues: 0 loop : -1.27 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 77 TYR 0.016 0.002 TYR A 40 PHE 0.008 0.002 PHE P 52 TRP 0.007 0.001 TRP R 94 HIS 0.002 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00347 (34074) covalent geometry : angle 0.58014 (45970) hydrogen bonds : bond 0.11982 ( 2391) hydrogen bonds : angle 3.84579 ( 7173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 362 time to evaluate : 1.509 Fit side-chains REVERT: A 120 LYS cc_start: 0.8663 (tttm) cc_final: 0.8457 (ttmp) REVERT: B 64 ARG cc_start: 0.8135 (tpt-90) cc_final: 0.7757 (ttm170) REVERT: H 64 ARG cc_start: 0.8237 (tpt-90) cc_final: 0.7798 (ttm170) outliers start: 45 outliers final: 28 residues processed: 364 average time/residue: 1.0365 time to fit residues: 424.7514 Evaluate side-chains 389 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 361 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 159 MET Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 95 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 318 optimal weight: 0.0670 chunk 97 optimal weight: 0.0010 chunk 381 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 338 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 overall best weight: 5.0130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 140 ASN G 140 ASN I 140 ASN M 140 ASN Q 140 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.097034 restraints weight = 87922.418| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.79 r_work: 0.2961 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 34074 Z= 0.273 Angle : 0.676 6.805 45970 Z= 0.391 Chirality : 0.046 0.145 4858 Planarity : 0.004 0.028 6068 Dihedral : 4.482 22.873 4494 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.53 % Allowed : 10.18 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.41 (0.12), residues: 4066 helix: 3.22 (0.08), residues: 3130 sheet: None (None), residues: 0 loop : -1.39 (0.15), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 77 TYR 0.020 0.003 TYR L 40 PHE 0.012 0.003 PHE A 56 TRP 0.007 0.001 TRP K 94 HIS 0.002 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00495 (34074) covalent geometry : angle 0.67644 (45970) hydrogen bonds : bond 0.14471 ( 2391) hydrogen bonds : angle 4.06036 ( 7173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 407 time to evaluate : 1.370 Fit side-chains REVERT: A 120 LYS cc_start: 0.8731 (tttm) cc_final: 0.8531 (ttmp) REVERT: B 64 ARG cc_start: 0.8239 (tpt-90) cc_final: 0.7743 (ttm170) REVERT: H 64 ARG cc_start: 0.8265 (tpt-90) cc_final: 0.7772 (ttm170) outliers start: 54 outliers final: 31 residues processed: 410 average time/residue: 1.1672 time to fit residues: 536.6168 Evaluate side-chains 417 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 386 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain N residue 159 MET Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 120 LYS Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 120 LYS Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain U residue 120 LYS Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain X residue 120 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 165 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 chunk 345 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 379 optimal weight: 4.9990 chunk 364 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 113 GLN B 15 GLN B 113 GLN C 15 GLN C 113 GLN D 15 GLN E 15 GLN E 113 GLN F 15 GLN F 113 GLN G 15 GLN H 15 GLN H 113 GLN I 15 GLN I 113 GLN J 15 GLN J 113 GLN K 15 GLN K 113 GLN L 15 GLN L 113 GLN M 15 GLN M 113 GLN N 15 GLN N 113 GLN O 15 GLN O 113 GLN P 15 GLN P 113 GLN Q 15 GLN Q 113 GLN R 15 GLN R 113 GLN S 15 GLN S 113 GLN T 15 GLN T 113 GLN U 15 GLN U 113 GLN V 15 GLN V 113 GLN W 15 GLN W 113 GLN X 15 GLN X 113 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.097419 restraints weight = 85147.652| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.76 r_work: 0.2970 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 34074 Z= 0.267 Angle : 0.668 6.679 45970 Z= 0.386 Chirality : 0.045 0.139 4858 Planarity : 0.004 0.025 6068 Dihedral : 4.461 22.808 4494 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.58 % Allowed : 9.50 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.31 (0.12), residues: 4066 helix: 3.16 (0.08), residues: 3130 sheet: None (None), residues: 0 loop : -1.47 (0.15), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 77 TYR 0.020 0.003 TYR S 40 PHE 0.011 0.003 PHE W 56 TRP 0.008 0.001 TRP K 94 HIS 0.002 0.001 HIS Q 14 Details of bonding type rmsd covalent geometry : bond 0.00481 (34074) covalent geometry : angle 0.66808 (45970) hydrogen bonds : bond 0.14231 ( 2391) hydrogen bonds : angle 4.04765 ( 7173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 402 time to evaluate : 1.391 Fit side-chains REVERT: B 64 ARG cc_start: 0.8240 (tpt-90) cc_final: 0.7759 (ttm170) REVERT: H 64 ARG cc_start: 0.8253 (tpt-90) cc_final: 0.7792 (ttm170) outliers start: 56 outliers final: 34 residues processed: 404 average time/residue: 1.1313 time to fit residues: 512.4713 Evaluate side-chains 434 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 400 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain N residue 159 MET Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 120 LYS Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 120 LYS Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 120 LYS Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain U residue 120 LYS Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain X residue 120 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 46 optimal weight: 0.7980 chunk 330 optimal weight: 10.0000 chunk 383 optimal weight: 7.9990 chunk 306 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 389 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 370 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 193 optimal weight: 7.9990 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 15 GLN A 113 GLN B 113 GLN C 15 GLN D 15 GLN D 113 GLN E 15 GLN E 113 GLN F 15 GLN G 15 GLN G 113 GLN H 15 GLN H 113 GLN I 15 GLN J 15 GLN J 113 GLN K 15 GLN K 113 GLN L 15 GLN M 15 GLN N 15 GLN O 15 GLN O 113 GLN P 15 GLN P 113 GLN Q 15 GLN R 15 GLN R 113 GLN S 15 GLN S 113 GLN T 15 GLN T 113 GLN U 15 GLN U 113 GLN V 15 GLN V 113 GLN W 15 GLN W 113 GLN X 15 GLN X 113 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.103765 restraints weight = 74569.179| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.67 r_work: 0.3066 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34074 Z= 0.201 Angle : 0.554 5.760 45970 Z= 0.320 Chirality : 0.040 0.126 4858 Planarity : 0.003 0.020 6068 Dihedral : 4.216 22.507 4494 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.30 % Allowed : 9.92 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.95 (0.12), residues: 4066 helix: 3.61 (0.08), residues: 3130 sheet: None (None), residues: 0 loop : -1.23 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 77 TYR 0.015 0.002 TYR A 40 PHE 0.008 0.002 PHE X 52 TRP 0.009 0.002 TRP K 94 HIS 0.001 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00319 (34074) covalent geometry : angle 0.55363 (45970) hydrogen bonds : bond 0.11242 ( 2391) hydrogen bonds : angle 3.75303 ( 7173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 365 time to evaluate : 1.145 Fit side-chains REVERT: B 64 ARG cc_start: 0.8142 (tpt-90) cc_final: 0.7759 (ttm170) REVERT: H 64 ARG cc_start: 0.8190 (tpt-90) cc_final: 0.7811 (ttm170) REVERT: V 95 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7450 (pt0) outliers start: 46 outliers final: 13 residues processed: 367 average time/residue: 0.9912 time to fit residues: 408.1959 Evaluate side-chains 375 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 361 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 95 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 355 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 321 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107597 restraints weight = 74610.180| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.66 r_work: 0.3123 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34074 Z= 0.179 Angle : 0.515 6.120 45970 Z= 0.297 Chirality : 0.038 0.120 4858 Planarity : 0.003 0.020 6068 Dihedral : 4.083 22.178 4494 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.71 % Allowed : 11.16 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.33 (0.12), residues: 4066 helix: 3.89 (0.08), residues: 3130 sheet: None (None), residues: 0 loop : -1.12 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 80 TYR 0.013 0.002 TYR A 40 PHE 0.007 0.002 PHE H 52 TRP 0.010 0.002 TRP Q 94 HIS 0.001 0.000 HIS D 58 Details of bonding type rmsd covalent geometry : bond 0.00275 (34074) covalent geometry : angle 0.51472 (45970) hydrogen bonds : bond 0.09963 ( 2391) hydrogen bonds : angle 3.56830 ( 7173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 363 time to evaluate : 1.192 Fit side-chains REVERT: B 64 ARG cc_start: 0.8147 (tpt-90) cc_final: 0.7795 (ttm170) REVERT: H 64 ARG cc_start: 0.8204 (tpt-90) cc_final: 0.7763 (ttm170) outliers start: 25 outliers final: 21 residues processed: 367 average time/residue: 1.0218 time to fit residues: 421.1049 Evaluate side-chains 379 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 358 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 95 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 293 optimal weight: 10.0000 chunk 313 optimal weight: 9.9990 chunk 320 optimal weight: 10.0000 chunk 289 optimal weight: 0.0060 chunk 139 optimal weight: 8.9990 chunk 340 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 329 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 233 optimal weight: 6.9990 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.099371 restraints weight = 84983.564| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.76 r_work: 0.2997 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 34074 Z= 0.244 Angle : 0.622 6.306 45970 Z= 0.359 Chirality : 0.043 0.140 4858 Planarity : 0.003 0.023 6068 Dihedral : 4.312 23.063 4494 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.79 % Allowed : 11.22 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.87 (0.12), residues: 4066 helix: 3.55 (0.08), residues: 3130 sheet: None (None), residues: 0 loop : -1.22 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 77 TYR 0.017 0.002 TYR F 40 PHE 0.010 0.002 PHE V 56 TRP 0.007 0.001 TRP L 94 HIS 0.002 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00422 (34074) covalent geometry : angle 0.62217 (45970) hydrogen bonds : bond 0.13236 ( 2391) hydrogen bonds : angle 3.94283 ( 7173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 362 time to evaluate : 0.937 Fit side-chains REVERT: B 64 ARG cc_start: 0.8217 (tpt-90) cc_final: 0.7728 (ttm170) REVERT: C 95 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7483 (pt0) REVERT: H 64 ARG cc_start: 0.8256 (tpt-90) cc_final: 0.7785 (ttm170) REVERT: V 95 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7554 (pt0) outliers start: 28 outliers final: 24 residues processed: 367 average time/residue: 0.9898 time to fit residues: 408.0346 Evaluate side-chains 388 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 362 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain X residue 96 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 163 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 263 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 287 optimal weight: 0.0070 chunk 209 optimal weight: 0.8980 chunk 272 optimal weight: 0.0870 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118426 restraints weight = 86682.182| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.78 r_work: 0.3271 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 34074 Z= 0.142 Angle : 0.463 5.954 45970 Z= 0.266 Chirality : 0.036 0.119 4858 Planarity : 0.002 0.020 6068 Dihedral : 3.903 21.293 4494 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.76 % Allowed : 10.80 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.76 (0.12), residues: 4066 helix: 4.12 (0.08), residues: 3154 sheet: None (None), residues: 0 loop : -0.76 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 157 TYR 0.014 0.001 TYR A 138 PHE 0.005 0.001 PHE Q 171 TRP 0.017 0.003 TRP S 94 HIS 0.002 0.000 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00217 (34074) covalent geometry : angle 0.46253 (45970) hydrogen bonds : bond 0.07124 ( 2391) hydrogen bonds : angle 3.28335 ( 7173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 419 time to evaluate : 1.638 Fit side-chains REVERT: A 95 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7510 (pt0) REVERT: B 64 ARG cc_start: 0.8134 (tpt-90) cc_final: 0.7784 (ttm170) REVERT: F 120 LYS cc_start: 0.8409 (tttp) cc_final: 0.8111 (tttm) REVERT: H 64 ARG cc_start: 0.8202 (tpt-90) cc_final: 0.7837 (ttm170) REVERT: I 120 LYS cc_start: 0.8423 (ttmp) cc_final: 0.8126 (tttm) REVERT: L 120 LYS cc_start: 0.8430 (tttp) cc_final: 0.8136 (tttm) REVERT: M 120 LYS cc_start: 0.8412 (tttp) cc_final: 0.8121 (tttm) REVERT: Q 120 LYS cc_start: 0.8414 (ttmp) cc_final: 0.8115 (tttm) REVERT: W 95 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7299 (pt0) REVERT: X 95 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7281 (pt0) outliers start: 27 outliers final: 16 residues processed: 424 average time/residue: 1.0212 time to fit residues: 493.2837 Evaluate side-chains 394 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 375 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 96 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 109 optimal weight: 8.9990 chunk 302 optimal weight: 0.7980 chunk 391 optimal weight: 0.0870 chunk 128 optimal weight: 10.0000 chunk 132 optimal weight: 0.0980 chunk 374 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 398 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 289 optimal weight: 4.9990 overall best weight: 1.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN C 126 ASN D 126 ASN E 126 ASN G 126 ASN H 126 ASN J 126 ASN K 126 ASN N 126 ASN O 126 ASN P 126 ASN R 126 ASN S 126 ASN T 126 ASN U 126 ASN W 126 ASN X 126 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112799 restraints weight = 86448.766| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.69 r_work: 0.3195 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 34074 Z= 0.158 Angle : 0.476 5.920 45970 Z= 0.273 Chirality : 0.036 0.119 4858 Planarity : 0.002 0.020 6068 Dihedral : 3.944 21.450 4494 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.62 % Allowed : 12.32 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.85 (0.12), residues: 4066 helix: 4.17 (0.08), residues: 3154 sheet: None (None), residues: 0 loop : -0.69 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 64 TYR 0.011 0.002 TYR A 55 PHE 0.008 0.001 PHE U 52 TRP 0.010 0.002 TRP L 94 HIS 0.001 0.000 HIS C 119 Details of bonding type rmsd covalent geometry : bond 0.00238 (34074) covalent geometry : angle 0.47608 (45970) hydrogen bonds : bond 0.08590 ( 2391) hydrogen bonds : angle 3.34978 ( 7173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14892.43 seconds wall clock time: 253 minutes 36.94 seconds (15216.94 seconds total)