Starting phenix.real_space_refine on Sat Jun 28 01:16:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m52_30083/06_2025/6m52_30083.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m52_30083/06_2025/6m52_30083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m52_30083/06_2025/6m52_30083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m52_30083/06_2025/6m52_30083.map" model { file = "/net/cci-nas-00/data/ceres_data/6m52_30083/06_2025/6m52_30083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m52_30083/06_2025/6m52_30083.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 66 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 23.92, per 1000 atoms: 0.72 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: 7.01 Conformation dependent library (CDL) restraints added in 5.2 seconds 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: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 14 through 42 removed outlier: 3.833A pdb=" N ASN A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 42 " --> pdb=" O MET A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 78 removed outlier: 3.572A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 78 " --> pdb=" O GLN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 125 removed outlier: 3.641A pdb=" N ASN A 110 " --> pdb=" O HIS A 106 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 138 through 160 removed outlier: 3.795A pdb=" N GLN A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 175 removed outlier: 4.029A pdb=" N GLU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 42 removed outlier: 3.766A pdb=" N ASN B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 42 " --> pdb=" O MET B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 78 removed outlier: 3.529A pdb=" N ALA B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 125 removed outlier: 3.744A pdb=" N ALA B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 110 " --> pdb=" O HIS B 106 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.869A pdb=" N GLN B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 175 removed outlier: 4.029A pdb=" N GLU B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 42 removed outlier: 3.760A pdb=" N ASN C 26 " --> pdb=" O ASN C 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 78 removed outlier: 3.529A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU C 65 " --> pdb=" O HIS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 125 removed outlier: 3.609A pdb=" N ASN C 110 " --> pdb=" O HIS C 106 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.880A pdb=" N GLN C 142 " --> pdb=" O TYR C 138 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 175 removed outlier: 4.003A pdb=" N GLU C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 42 removed outlier: 3.759A pdb=" N ASN D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 78 removed outlier: 3.530A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D 65 " --> pdb=" O HIS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 removed outlier: 3.750A pdb=" N ALA D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.894A pdb=" N GLN D 142 " --> pdb=" O TYR D 138 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 175 removed outlier: 3.987A pdb=" N GLU D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 42 removed outlier: 3.765A pdb=" N ASN E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE E 42 " --> pdb=" O MET E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 78 removed outlier: 3.528A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU E 65 " --> pdb=" O HIS E 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY E 78 " --> pdb=" O GLN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 125 removed outlier: 3.744A pdb=" N ALA E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET E 101 " --> pdb=" O GLY E 97 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN E 110 " --> pdb=" O HIS E 106 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.885A pdb=" N GLN E 142 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 175 removed outlier: 4.030A pdb=" N GLU E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 42 removed outlier: 3.759A pdb=" N ASN F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE F 42 " --> pdb=" O MET F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 78 removed outlier: 3.529A pdb=" N ALA F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG F 64 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY F 78 " --> pdb=" O GLN F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 125 removed outlier: 3.616A pdb=" N ASN F 110 " --> pdb=" O HIS F 106 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.880A pdb=" N GLN F 142 " --> pdb=" O TYR F 138 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 175 removed outlier: 3.993A pdb=" N GLU F 168 " --> pdb=" O SER F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 42 removed outlier: 3.760A pdb=" N ASN G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 78 removed outlier: 3.529A pdb=" N ALA G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG G 64 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU G 65 " --> pdb=" O HIS G 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 78 " --> pdb=" O GLN G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 125 removed outlier: 3.759A pdb=" N ALA G 100 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET G 101 " --> pdb=" O GLY G 97 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN G 110 " --> pdb=" O HIS G 106 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.898A pdb=" N GLN G 142 " --> pdb=" O TYR G 138 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 175 removed outlier: 3.980A pdb=" N GLU G 168 " --> pdb=" O SER G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 42 removed outlier: 3.767A pdb=" N ASN H 26 " --> pdb=" O ASN H 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE H 42 " --> pdb=" O MET H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 78 removed outlier: 3.528A pdb=" N ALA H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG H 64 " --> pdb=" O SER H 60 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU H 65 " --> pdb=" O HIS H 61 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY H 78 " --> pdb=" O GLN H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 125 removed outlier: 3.738A pdb=" N ALA H 100 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET H 101 " --> pdb=" O GLY H 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN H 110 " --> pdb=" O HIS H 106 " (cutoff:3.500A) removed outlier: 3.590A 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: 3.878A pdb=" N GLN H 142 " --> pdb=" O TYR H 138 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY H 160 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 175 removed outlier: 4.018A pdb=" N GLU H 168 " --> pdb=" O SER H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 42 removed outlier: 3.761A pdb=" N ASN I 26 " --> pdb=" O ASN I 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE I 42 " --> pdb=" O MET I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 78 removed outlier: 3.529A pdb=" N ALA I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU I 65 " --> pdb=" O HIS I 61 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY I 78 " --> pdb=" O GLN I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 125 removed outlier: 3.776A pdb=" N ALA I 100 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET I 101 " --> pdb=" O GLY I 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN I 110 " --> pdb=" O HIS I 106 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.891A pdb=" N GLN I 142 " --> pdb=" O TYR I 138 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL I 143 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY I 160 " --> pdb=" O LEU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 175 removed outlier: 3.978A pdb=" N GLU I 168 " --> pdb=" O SER I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 42 removed outlier: 3.766A pdb=" N ASN J 26 " --> pdb=" O ASN J 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE J 42 " --> pdb=" O MET J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 78 removed outlier: 3.531A pdb=" N ALA J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU J 65 " --> pdb=" O HIS J 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY J 78 " --> pdb=" O GLN J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.744A pdb=" N ALA J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET J 101 " --> pdb=" O GLY J 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN J 110 " --> pdb=" O HIS J 106 " (cutoff:3.500A) removed outlier: 3.590A 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: 3.883A pdb=" N GLN J 142 " --> pdb=" O TYR J 138 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY J 160 " --> pdb=" O LEU J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 175 removed outlier: 4.043A pdb=" N GLU J 168 " --> pdb=" O SER J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 42 removed outlier: 3.765A pdb=" N ASN K 26 " --> pdb=" O ASN K 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE K 42 " --> pdb=" O MET K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 78 removed outlier: 3.530A pdb=" N ALA K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU K 65 " --> pdb=" O HIS K 61 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY K 78 " --> pdb=" O GLN K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 125 removed outlier: 3.744A pdb=" N ALA K 100 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET K 101 " --> pdb=" O GLY K 97 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN K 110 " --> pdb=" O HIS K 106 " (cutoff:3.500A) removed outlier: 3.593A 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: 3.884A pdb=" N GLN K 142 " --> pdb=" O TYR K 138 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL K 143 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY K 160 " --> pdb=" O LEU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 175 removed outlier: 4.043A pdb=" N GLU K 168 " --> pdb=" O SER K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 42 removed outlier: 3.760A pdb=" N ASN L 26 " --> pdb=" O ASN L 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE L 42 " --> pdb=" O MET L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 78 removed outlier: 3.529A pdb=" N ALA L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG L 64 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU L 65 " --> pdb=" O HIS L 61 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY L 78 " --> pdb=" O GLN L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 125 removed outlier: 3.775A pdb=" N ALA L 100 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET L 101 " --> pdb=" O GLY L 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN L 110 " --> pdb=" O HIS L 106 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.877A pdb=" N GLN L 142 " --> pdb=" O TYR L 138 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 175 removed outlier: 3.978A pdb=" N GLU L 168 " --> pdb=" O SER L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 42 removed outlier: 3.760A pdb=" N ASN M 26 " --> pdb=" O ASN M 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE M 42 " --> pdb=" O MET M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 78 removed outlier: 3.529A pdb=" N ALA M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG M 64 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU M 65 " --> pdb=" O HIS M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 125 removed outlier: 3.750A pdb=" N ALA M 100 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET M 101 " --> pdb=" O GLY M 97 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN M 110 " --> pdb=" O HIS M 106 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.895A pdb=" N GLN M 142 " --> pdb=" O TYR M 138 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL M 143 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY M 160 " --> pdb=" O LEU M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 175 removed outlier: 4.004A pdb=" N GLU M 168 " --> pdb=" O SER M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 42 removed outlier: 3.760A pdb=" N ASN N 26 " --> pdb=" O ASN N 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE N 42 " --> pdb=" O MET N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 78 removed outlier: 3.529A pdb=" N ALA N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG N 64 " --> pdb=" O SER N 60 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU N 65 " --> pdb=" O HIS N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 125 removed outlier: 3.752A pdb=" N ALA N 100 " --> pdb=" O SER N 96 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET N 101 " --> pdb=" O GLY N 97 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN N 110 " --> pdb=" O HIS N 106 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.880A pdb=" N GLN N 142 " --> pdb=" O TYR N 138 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL N 143 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY N 160 " --> pdb=" O LEU N 156 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 175 removed outlier: 4.003A pdb=" N GLU N 168 " --> pdb=" O SER N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 42 removed outlier: 3.765A pdb=" N ASN O 26 " --> pdb=" O ASN O 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE O 42 " --> pdb=" O MET O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 78 removed outlier: 3.530A pdb=" N ALA O 53 " --> pdb=" O LEU O 49 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG O 64 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU O 65 " --> pdb=" O HIS O 61 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY O 78 " --> pdb=" O GLN O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 125 removed outlier: 3.743A pdb=" N ALA O 100 " --> pdb=" O SER O 96 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET O 101 " --> pdb=" O GLY O 97 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN O 110 " --> pdb=" O HIS O 106 " (cutoff:3.500A) removed outlier: 3.588A 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: 3.886A pdb=" N GLN O 142 " --> pdb=" O TYR O 138 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL O 143 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 175 removed outlier: 4.029A pdb=" N GLU O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 42 removed outlier: 3.765A pdb=" N ASN P 26 " --> pdb=" O ASN P 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE P 42 " --> pdb=" O MET P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 78 removed outlier: 3.529A pdb=" N ALA P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG P 64 " --> pdb=" O SER P 60 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU P 65 " --> pdb=" O HIS P 61 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY P 78 " --> pdb=" O GLN P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 125 removed outlier: 3.743A pdb=" N ALA P 100 " --> pdb=" O SER P 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET P 101 " --> pdb=" O GLY P 97 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN P 110 " --> pdb=" O HIS P 106 " (cutoff:3.500A) removed outlier: 3.590A 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: 3.877A pdb=" N GLN P 142 " --> pdb=" O TYR P 138 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL P 143 " --> pdb=" O LEU P 139 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY P 160 " --> pdb=" O LEU P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 175 removed outlier: 4.030A pdb=" N GLU P 168 " --> pdb=" O SER P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 42 removed outlier: 3.759A pdb=" N ASN Q 26 " --> pdb=" O ASN Q 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 78 removed outlier: 3.529A pdb=" N ALA Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG Q 64 " --> pdb=" O SER Q 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU Q 65 " --> pdb=" O HIS Q 61 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY Q 78 " --> pdb=" O GLN Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 125 removed outlier: 3.747A pdb=" N ALA Q 100 " --> pdb=" O SER Q 96 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.594A 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: 3.892A pdb=" N GLN Q 142 " --> pdb=" O TYR Q 138 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY Q 160 " --> pdb=" O LEU Q 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 175 removed outlier: 4.004A pdb=" N GLU Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 42 removed outlier: 3.765A pdb=" N ASN R 26 " --> pdb=" O ASN R 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE R 42 " --> pdb=" O MET R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 78 removed outlier: 3.528A pdb=" N ALA R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU R 65 " --> pdb=" O HIS R 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY R 78 " --> pdb=" O GLN R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 125 removed outlier: 3.744A pdb=" N ALA R 100 " --> pdb=" O SER R 96 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET R 101 " --> pdb=" O GLY R 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN R 110 " --> pdb=" O HIS R 106 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.887A pdb=" N GLN R 142 " --> pdb=" O TYR R 138 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL R 143 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 175 removed outlier: 4.029A pdb=" N GLU R 168 " --> pdb=" O SER R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 42 removed outlier: 3.765A pdb=" N ASN S 26 " --> pdb=" O ASN S 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE S 42 " --> pdb=" O MET S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 78 removed outlier: 3.528A pdb=" N ALA S 53 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG S 64 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU S 65 " --> pdb=" O HIS S 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY S 78 " --> pdb=" O GLN S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 125 removed outlier: 3.539A pdb=" N ALA S 100 " --> pdb=" O SER S 96 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN S 110 " --> pdb=" O HIS S 106 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.875A pdb=" N GLN S 142 " --> pdb=" O TYR S 138 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL S 143 " --> pdb=" O LEU S 139 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY S 160 " --> pdb=" O LEU S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 164 through 175 removed outlier: 4.018A pdb=" N GLU S 168 " --> pdb=" O SER S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 42 removed outlier: 3.765A pdb=" N ASN T 26 " --> pdb=" O ASN T 22 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR T 40 " --> pdb=" O LEU T 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE T 42 " --> pdb=" O MET T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 78 removed outlier: 3.530A pdb=" N ALA T 53 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG T 64 " --> pdb=" O SER T 60 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU T 65 " --> pdb=" O HIS T 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY T 78 " --> pdb=" O GLN T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 125 removed outlier: 3.738A pdb=" N ALA T 100 " --> pdb=" O SER T 96 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET T 101 " --> pdb=" O GLY T 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN T 110 " --> pdb=" O HIS T 106 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.891A pdb=" N GLN T 142 " --> pdb=" O TYR T 138 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL T 143 " --> pdb=" O LEU T 139 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY T 160 " --> pdb=" O LEU T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 175 removed outlier: 4.030A pdb=" N GLU T 168 " --> pdb=" O SER T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 42 removed outlier: 3.765A pdb=" N ASN U 26 " --> pdb=" O ASN U 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE U 42 " --> pdb=" O MET U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 78 removed outlier: 3.531A pdb=" N ALA U 53 " --> pdb=" O LEU U 49 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG U 64 " --> pdb=" O SER U 60 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY U 78 " --> pdb=" O GLN U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 125 removed outlier: 3.539A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN U 110 " --> pdb=" O HIS U 106 " (cutoff:3.500A) removed outlier: 3.593A 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: 3.875A pdb=" N GLN U 142 " --> pdb=" O TYR U 138 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL U 143 " --> pdb=" O LEU U 139 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY U 160 " --> pdb=" O LEU U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 175 removed outlier: 4.043A pdb=" N GLU U 168 " --> pdb=" O SER U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 42 removed outlier: 3.765A pdb=" N ASN V 26 " --> pdb=" O ASN V 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR V 40 " --> pdb=" O LEU V 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE V 42 " --> pdb=" O MET V 38 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 78 removed outlier: 3.528A pdb=" N ALA V 53 " --> pdb=" O LEU V 49 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG V 64 " --> pdb=" O SER V 60 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY V 78 " --> pdb=" O GLN V 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 125 removed outlier: 3.543A pdb=" N ALA V 100 " --> pdb=" O SER V 96 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN V 110 " --> pdb=" O HIS V 106 " (cutoff:3.500A) removed outlier: 3.587A 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: 3.876A pdb=" N GLN V 142 " --> pdb=" O TYR V 138 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL V 143 " --> pdb=" O LEU V 139 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY V 160 " --> pdb=" O LEU V 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 164 through 175 removed outlier: 3.993A pdb=" N GLU V 168 " --> pdb=" O SER V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 42 removed outlier: 3.766A pdb=" N ASN W 26 " --> pdb=" O ASN W 22 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR W 40 " --> pdb=" O LEU W 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE W 42 " --> pdb=" O MET W 38 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 78 removed outlier: 3.528A pdb=" N ALA W 53 " --> pdb=" O LEU W 49 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG W 64 " --> pdb=" O SER W 60 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU W 65 " --> pdb=" O HIS W 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY W 78 " --> pdb=" O GLN W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 125 removed outlier: 3.626A pdb=" N ASN W 110 " --> pdb=" O HIS W 106 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.867A pdb=" N GLN W 142 " --> pdb=" O TYR W 138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY W 160 " --> pdb=" O LEU W 156 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 175 removed outlier: 3.992A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 42 removed outlier: 3.765A pdb=" N ASN X 26 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR X 40 " --> pdb=" O LEU X 36 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE X 42 " --> pdb=" O MET X 38 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 78 removed outlier: 3.531A pdb=" N ALA X 53 " --> pdb=" O LEU X 49 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU X 65 " --> pdb=" O HIS X 61 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY X 78 " --> pdb=" O GLN X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 125 removed outlier: 3.610A pdb=" N ASN X 110 " --> pdb=" O HIS X 106 " (cutoff:3.500A) removed outlier: 3.593A 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: 3.865A pdb=" N GLN X 142 " --> pdb=" O TYR X 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL X 143 " --> pdb=" O LEU X 139 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY X 160 " --> pdb=" O LEU X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 175 removed outlier: 4.042A pdb=" N GLU X 168 " --> pdb=" O SER X 164 " (cutoff:3.500A) 2346 hydrogen bonds defined for protein. 7038 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: 9.60 Time building geometry restraints manager: 8.49 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: 9779 1.33 - 1.45: 5585 1.45 - 1.57: 18446 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34074 Sorted by residual: bond pdb=" CB GLU F 65 " pdb=" CG GLU F 65 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.54e+00 bond pdb=" CB GLU Q 65 " pdb=" CG GLU Q 65 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.45e+00 bond pdb=" CB GLU N 65 " pdb=" CG GLU N 65 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CB GLU M 65 " pdb=" CG GLU M 65 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.41e+00 ... (remaining 34069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 43015 1.72 - 3.45: 2464 3.45 - 5.17: 417 5.17 - 6.90: 51 6.90 - 8.62: 23 Bond angle restraints: 45970 Sorted by residual: angle pdb=" N GLU I 95 " pdb=" CA GLU I 95 " pdb=" CB GLU I 95 " ideal model delta sigma weight residual 114.17 107.88 6.29 1.14e+00 7.69e-01 3.05e+01 angle pdb=" N GLU L 95 " pdb=" CA GLU L 95 " pdb=" CB GLU L 95 " ideal model delta sigma weight residual 114.17 107.90 6.27 1.14e+00 7.69e-01 3.02e+01 angle pdb=" C TRP F 94 " pdb=" N GLU F 95 " pdb=" CA GLU F 95 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" N GLU U 95 " pdb=" CA GLU U 95 " pdb=" C GLU U 95 " ideal model delta sigma weight residual 110.80 119.33 -8.53 2.13e+00 2.20e-01 1.60e+01 angle pdb=" N GLU S 95 " pdb=" CA GLU S 95 " pdb=" C GLU S 95 " ideal model delta sigma weight residual 110.80 119.31 -8.51 2.13e+00 2.20e-01 1.60e+01 ... (remaining 45965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 18044 17.12 - 34.24: 2012 34.24 - 51.36: 365 51.36 - 68.48: 100 68.48 - 85.60: 41 Dihedral angle restraints: 20562 sinusoidal: 8354 harmonic: 12208 Sorted by residual: dihedral pdb=" CA TRP Q 94 " pdb=" C TRP Q 94 " pdb=" N GLU Q 95 " pdb=" CA GLU Q 95 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TRP E 94 " pdb=" C TRP E 94 " pdb=" N GLU E 95 " pdb=" CA GLU E 95 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA TRP B 94 " pdb=" C TRP B 94 " pdb=" N GLU B 95 " pdb=" CA GLU B 95 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 20559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3333 0.055 - 0.110: 1183 0.110 - 0.164: 312 0.164 - 0.219: 17 0.219 - 0.274: 13 Chirality restraints: 4858 Sorted by residual: chirality pdb=" CG LEU K 73 " pdb=" CB LEU K 73 " pdb=" CD1 LEU K 73 " pdb=" CD2 LEU K 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CG LEU R 73 " pdb=" CB LEU R 73 " pdb=" CD1 LEU R 73 " pdb=" CD2 LEU R 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CG LEU E 73 " pdb=" CB LEU E 73 " pdb=" CD1 LEU E 73 " pdb=" CD2 LEU E 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 4855 not shown) Planarity restraints: 6068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR W 33 " -0.031 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CG TYR W 33 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR W 33 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR W 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR W 33 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR W 33 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR W 33 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR W 33 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 33 " 0.031 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CG TYR S 33 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR S 33 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR S 33 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 33 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR S 33 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR S 33 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR S 33 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 33 " -0.031 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CG TYR V 33 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR V 33 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR V 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR V 33 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR V 33 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR V 33 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR V 33 " -0.008 2.00e-02 2.50e+03 ... (remaining 6065 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 10841 2.89 - 3.39: 30052 3.39 - 3.90: 52078 3.90 - 4.40: 61772 4.40 - 4.90: 103364 Nonbonded interactions: 258107 Sorted by model distance: nonbonded pdb=" N ASP E 46 " pdb=" OD1 ASP E 46 " model vdw 2.390 3.120 nonbonded pdb=" N ASP R 46 " pdb=" OD1 ASP R 46 " model vdw 2.391 3.120 nonbonded pdb=" N ASP T 46 " pdb=" OD1 ASP T 46 " model vdw 2.391 3.120 nonbonded pdb=" N ASP W 46 " pdb=" OD1 ASP W 46 " model vdw 2.392 3.120 nonbonded pdb=" N ASP S 46 " pdb=" OD1 ASP S 46 " model vdw 2.392 3.120 ... (remaining 258102 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: 0.04 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.140 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 71.960 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.009 0.049 34074 Z= 0.407 Angle : 0.942 8.625 45970 Z= 0.568 Chirality : 0.059 0.274 4858 Planarity : 0.005 0.042 6068 Dihedral : 15.324 85.598 12670 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 4066 helix: 0.61 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -2.58 (0.14), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP Q 94 HIS 0.006 0.001 HIS J 61 PHE 0.013 0.003 PHE L 171 TYR 0.055 0.004 TYR W 33 ARG 0.003 0.001 ARG U 10 Details of bonding type rmsd hydrogen bonds : bond 0.20834 ( 2346) hydrogen bonds : angle 5.00722 ( 7038) covalent geometry : bond 0.00927 (34074) covalent geometry : angle 0.94233 (45970) *********************** 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 392 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 4.139 Fit side-chains REVERT: A 62 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6804 (mm-30) REVERT: B 62 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6619 (mm-30) REVERT: B 64 ARG cc_start: 0.7103 (tpt170) cc_final: 0.6244 (ttm170) REVERT: E 62 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6868 (mm-30) REVERT: F 62 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6827 (mm-30) REVERT: G 62 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6684 (mm-30) REVERT: H 62 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6703 (mm-30) REVERT: H 64 ARG cc_start: 0.7187 (tpt170) cc_final: 0.6333 (ttm170) REVERT: I 62 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6696 (mm-30) REVERT: J 120 LYS cc_start: 0.8114 (ttpp) cc_final: 0.7648 (ttmm) REVERT: K 120 LYS cc_start: 0.7967 (ttpp) cc_final: 0.7492 (ttmm) REVERT: L 62 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6621 (mm-30) REVERT: O 62 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6628 (mm-30) REVERT: P 62 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6623 (mm-30) REVERT: Q 62 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6633 (mm-30) REVERT: R 62 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6806 (mm-30) REVERT: S 62 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6670 (mm-30) REVERT: T 62 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6462 (mm-30) REVERT: U 62 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6864 (mm-30) REVERT: U 120 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7631 (ttmm) REVERT: V 62 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6653 (mm-30) REVERT: W 62 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6619 (mm-30) REVERT: X 62 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6644 (mm-30) REVERT: X 120 LYS cc_start: 0.7908 (ttpp) cc_final: 0.7432 (ttmm) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 2.6538 time to fit residues: 1157.3381 Evaluate side-chains 321 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 4.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 3.9990 chunk 309 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 370 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN E 51 ASN H 51 ASN J 51 ASN O 51 ASN P 51 ASN Q 51 ASN T 51 ASN U 51 ASN V 51 ASN V 110 ASN W 51 ASN W 110 ASN X 51 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124737 restraints weight = 91109.495| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.11 r_work: 0.3391 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 34074 Z= 0.145 Angle : 0.477 6.334 45970 Z= 0.274 Chirality : 0.036 0.135 4858 Planarity : 0.003 0.025 6068 Dihedral : 4.050 22.197 4494 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.93 % Allowed : 3.67 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.12), residues: 4066 helix: 2.98 (0.08), residues: 3082 sheet: None (None), residues: 0 loop : -1.73 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 94 HIS 0.003 0.001 HIS G 58 PHE 0.007 0.001 PHE L 171 TYR 0.012 0.001 TYR A 55 ARG 0.002 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.07792 ( 2346) hydrogen bonds : angle 3.47457 ( 7038) covalent geometry : bond 0.00222 (34074) covalent geometry : angle 0.47678 (45970) *********************** 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 547 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 514 time to evaluate : 3.742 Fit side-chains REVERT: A 62 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7953 (mm-30) REVERT: B 62 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7866 (mm-30) REVERT: B 64 ARG cc_start: 0.7986 (tpt170) cc_final: 0.7578 (ttm170) REVERT: B 157 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7592 (mtt-85) REVERT: C 157 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7709 (mtt-85) REVERT: D 157 ARG cc_start: 0.8031 (mtt180) cc_final: 0.7754 (mtt-85) REVERT: E 62 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7890 (mm-30) REVERT: E 157 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7611 (mtt-85) REVERT: F 62 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7908 (mm-30) REVERT: F 157 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7682 (mtt-85) REVERT: G 62 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7921 (mm-30) REVERT: G 157 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7694 (mtt-85) REVERT: H 62 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7874 (mm-30) REVERT: H 64 ARG cc_start: 0.8032 (tpt170) cc_final: 0.7554 (ttm170) REVERT: H 157 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7575 (mtt-85) REVERT: I 62 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7883 (mm-30) REVERT: J 157 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7606 (mtt-85) REVERT: K 157 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7641 (mtt-85) REVERT: L 62 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7849 (mm-30) REVERT: L 157 ARG cc_start: 0.8005 (mtt180) cc_final: 0.7730 (mtt-85) REVERT: M 157 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7738 (mtt-85) REVERT: N 157 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7722 (mtt-85) REVERT: O 62 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7907 (mm-30) REVERT: O 157 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7616 (mtt-85) REVERT: P 62 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7902 (mm-30) REVERT: P 157 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7598 (mtt-85) REVERT: Q 62 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7926 (mm-30) REVERT: Q 173 LYS cc_start: 0.8457 (tptt) cc_final: 0.8246 (tppt) REVERT: R 62 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7898 (mm-30) REVERT: R 157 ARG cc_start: 0.7955 (mtt180) cc_final: 0.7594 (mtt-85) REVERT: S 62 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7897 (mm-30) REVERT: S 95 GLU cc_start: 0.7416 (tt0) cc_final: 0.7056 (mt-10) REVERT: T 62 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7852 (mm-30) REVERT: T 157 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7634 (mtt-85) REVERT: U 62 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7878 (mm-30) REVERT: U 95 GLU cc_start: 0.7470 (tt0) cc_final: 0.7099 (mt-10) REVERT: V 62 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7846 (mm-30) REVERT: V 95 GLU cc_start: 0.7541 (tt0) cc_final: 0.7164 (mt-10) REVERT: W 62 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7839 (mm-30) REVERT: X 62 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7908 (mm-30) outliers start: 33 outliers final: 0 residues processed: 546 average time/residue: 2.1241 time to fit residues: 1311.5108 Evaluate side-chains 312 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 3.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 345 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 275 optimal weight: 10.0000 chunk 402 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 225 optimal weight: 0.9990 chunk 338 optimal weight: 0.0970 chunk 285 optimal weight: 0.8980 chunk 288 optimal weight: 4.9990 chunk 396 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN C 51 ASN C 110 ASN D 51 ASN F 51 ASN K 51 ASN L 51 ASN M 51 ASN N 51 ASN R 51 ASN S 51 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122089 restraints weight = 74928.859| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.88 r_work: 0.3331 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2310 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= 0.145 Angle : 0.459 8.216 45970 Z= 0.265 Chirality : 0.035 0.148 4858 Planarity : 0.003 0.025 6068 Dihedral : 3.904 21.315 4494 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.48 % Allowed : 7.57 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.13), residues: 4066 helix: 3.74 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -1.28 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 94 HIS 0.002 0.000 HIS R 58 PHE 0.006 0.001 PHE M 171 TYR 0.012 0.001 TYR B 33 ARG 0.006 0.000 ARG S 64 Details of bonding type rmsd hydrogen bonds : bond 0.08042 ( 2346) hydrogen bonds : angle 3.30686 ( 7038) covalent geometry : bond 0.00225 (34074) covalent geometry : angle 0.45881 (45970) *********************** 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 440 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 423 time to evaluate : 6.602 Fit side-chains REVERT: A 62 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7996 (mm-30) REVERT: A 157 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7841 (mtt180) REVERT: B 62 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7930 (mm-30) REVERT: B 64 ARG cc_start: 0.8011 (tpt170) cc_final: 0.7574 (ttm170) REVERT: C 157 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7710 (mtt-85) REVERT: D 157 ARG cc_start: 0.8084 (mtt180) cc_final: 0.7760 (mtt-85) REVERT: E 62 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7961 (mm-30) REVERT: F 62 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7975 (mm-30) REVERT: G 62 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7993 (mm-30) REVERT: G 157 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7695 (mtt-85) REVERT: H 62 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7929 (mm-30) REVERT: H 64 ARG cc_start: 0.8025 (tpt170) cc_final: 0.7546 (ttm170) REVERT: I 62 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7949 (mm-30) REVERT: L 62 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7917 (mm-30) REVERT: L 157 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7732 (mtt-85) REVERT: M 157 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7733 (mtt-85) REVERT: N 157 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7716 (mtt-85) REVERT: O 62 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7950 (mm-30) REVERT: P 62 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7978 (mm-30) REVERT: Q 62 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7983 (mm-30) REVERT: R 62 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7960 (mm-30) REVERT: S 62 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7977 (mm-30) REVERT: S 95 GLU cc_start: 0.7567 (tt0) cc_final: 0.7259 (mt-10) REVERT: T 62 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7922 (mm-30) REVERT: U 62 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7946 (mm-30) REVERT: U 95 GLU cc_start: 0.7611 (tt0) cc_final: 0.7266 (mt-10) REVERT: V 62 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7929 (mm-30) REVERT: V 95 GLU cc_start: 0.7656 (tt0) cc_final: 0.7295 (mt-10) REVERT: W 62 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7916 (mm-30) REVERT: X 62 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7958 (mm-30) outliers start: 17 outliers final: 0 residues processed: 438 average time/residue: 2.0917 time to fit residues: 1051.0527 Evaluate side-chains 331 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 3 optimal weight: 10.0000 chunk 253 optimal weight: 0.1980 chunk 405 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 312 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 310 optimal weight: 3.9990 chunk 379 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 51 ASN I 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112737 restraints weight = 79209.107| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.97 r_work: 0.3213 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1792 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= 0.187 Angle : 0.536 7.920 45970 Z= 0.304 Chirality : 0.038 0.140 4858 Planarity : 0.003 0.025 6068 Dihedral : 4.062 21.607 4494 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.38 % Allowed : 9.95 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.99 (0.13), residues: 4066 helix: 3.69 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -1.26 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 94 HIS 0.003 0.001 HIS M 58 PHE 0.008 0.002 PHE I 171 TYR 0.014 0.002 TYR O 33 ARG 0.004 0.000 ARG S 64 Details of bonding type rmsd hydrogen bonds : bond 0.10570 ( 2346) hydrogen bonds : angle 3.61117 ( 7038) covalent geometry : bond 0.00321 (34074) covalent geometry : angle 0.53556 (45970) *********************** 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 479 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 430 time to evaluate : 6.193 Fit side-chains REVERT: A 62 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8035 (mm-30) REVERT: B 62 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7991 (mm-30) REVERT: B 64 ARG cc_start: 0.8153 (tpt170) cc_final: 0.7638 (ttm170) REVERT: E 62 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7992 (mm-30) REVERT: F 62 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8034 (mm-30) REVERT: G 62 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8039 (mm-30) REVERT: H 62 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7996 (mm-30) REVERT: H 64 ARG cc_start: 0.8158 (tpt170) cc_final: 0.7658 (ttm170) REVERT: H 95 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7940 (pt0) REVERT: I 62 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7999 (mm-30) REVERT: L 62 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8003 (mm-30) REVERT: O 62 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7981 (mm-30) REVERT: P 62 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7996 (mm-30) REVERT: Q 62 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8035 (mm-30) REVERT: R 62 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8018 (mm-30) REVERT: S 62 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8007 (mm-30) REVERT: S 95 GLU cc_start: 0.7662 (tt0) cc_final: 0.7371 (mt-10) REVERT: T 62 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7993 (mm-30) REVERT: U 62 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8000 (mm-30) REVERT: U 95 GLU cc_start: 0.7745 (tt0) cc_final: 0.7419 (mt-10) REVERT: V 62 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7982 (mm-30) REVERT: V 95 GLU cc_start: 0.7740 (tt0) cc_final: 0.7448 (mt-10) REVERT: W 62 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7995 (mm-30) REVERT: X 62 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8002 (mm-30) outliers start: 49 outliers final: 13 residues processed: 465 average time/residue: 1.9135 time to fit residues: 1029.3907 Evaluate side-chains 396 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 382 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain V residue 73 LEU Chi-restraints excluded: chain W residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 273 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 290 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 352 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 374 optimal weight: 9.9990 chunk 293 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 379 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.123626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.110448 restraints weight = 81369.687| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.98 r_work: 0.3152 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 34074 Z= 0.198 Angle : 0.554 7.745 45970 Z= 0.315 Chirality : 0.039 0.140 4858 Planarity : 0.003 0.025 6068 Dihedral : 4.138 21.809 4494 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.77 % Allowed : 10.91 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.13), residues: 4066 helix: 3.61 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -1.30 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP G 94 HIS 0.003 0.001 HIS D 58 PHE 0.008 0.002 PHE M 171 TYR 0.014 0.002 TYR O 33 ARG 0.003 0.000 ARG R 64 Details of bonding type rmsd hydrogen bonds : bond 0.11165 ( 2346) hydrogen bonds : angle 3.68029 ( 7038) covalent geometry : bond 0.00350 (34074) covalent geometry : angle 0.55449 (45970) *********************** 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 528 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 430 time to evaluate : 3.799 Fit side-chains REVERT: A 62 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8050 (mm-30) REVERT: B 15 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6100 (mm-40) REVERT: B 62 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8003 (mm-30) REVERT: B 64 ARG cc_start: 0.8182 (tpt170) cc_final: 0.7654 (ttm170) REVERT: E 15 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6075 (mm-40) REVERT: E 62 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8001 (mm-30) REVERT: F 62 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8058 (mm-30) REVERT: G 62 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8034 (mm-30) REVERT: H 62 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8031 (mm-30) REVERT: H 64 ARG cc_start: 0.8199 (tpt170) cc_final: 0.7672 (ttm170) REVERT: I 62 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8002 (mm-30) REVERT: J 15 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.6117 (mm-40) REVERT: K 15 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6082 (mm-40) REVERT: L 62 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8035 (mm-30) REVERT: O 62 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7995 (mm-30) REVERT: P 62 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8011 (mm-30) REVERT: Q 62 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8038 (mm-30) REVERT: R 15 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6071 (mm-40) REVERT: R 62 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8002 (mm-30) REVERT: S 62 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8031 (mm-30) REVERT: S 95 GLU cc_start: 0.7654 (tt0) cc_final: 0.7449 (mt-10) REVERT: T 15 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6081 (mm-40) REVERT: T 62 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7992 (mm-30) REVERT: U 62 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8007 (mm-30) REVERT: U 95 GLU cc_start: 0.7697 (tt0) cc_final: 0.7464 (mt-10) REVERT: V 62 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7990 (mm-30) REVERT: V 95 GLU cc_start: 0.7700 (tt0) cc_final: 0.7466 (mt-10) REVERT: W 62 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7997 (mm-30) REVERT: X 62 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8006 (mm-30) outliers start: 98 outliers final: 54 residues processed: 480 average time/residue: 1.7636 time to fit residues: 981.9435 Evaluate side-chains 461 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 401 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 126 ASN Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 126 ASN Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 15 GLN Chi-restraints excluded: chain K residue 126 ASN Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain M residue 126 ASN Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain N residue 126 ASN Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 126 ASN Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 126 ASN Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain T residue 15 GLN Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain T residue 139 LEU Chi-restraints excluded: chain U residue 126 ASN Chi-restraints excluded: chain U residue 139 LEU Chi-restraints excluded: chain V residue 73 LEU Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 126 ASN Chi-restraints excluded: chain W residue 139 LEU Chi-restraints excluded: chain X residue 126 ASN Chi-restraints excluded: chain X residue 139 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 402 optimal weight: 7.9990 chunk 372 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 224 optimal weight: 8.9990 chunk 405 optimal weight: 10.0000 chunk 148 optimal weight: 0.5980 chunk 330 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 343 optimal weight: 5.9990 chunk 352 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.128090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115627 restraints weight = 65949.760| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.77 r_work: 0.3263 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34074 Z= 0.168 Angle : 0.496 7.047 45970 Z= 0.284 Chirality : 0.037 0.133 4858 Planarity : 0.003 0.024 6068 Dihedral : 4.007 21.863 4494 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.05 % Allowed : 10.63 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.16 (0.13), residues: 4066 helix: 3.80 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -1.16 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 94 HIS 0.003 0.001 HIS D 58 PHE 0.007 0.001 PHE M 171 TYR 0.011 0.001 TYR A 55 ARG 0.003 0.000 ARG T 64 Details of bonding type rmsd hydrogen bonds : bond 0.09541 ( 2346) hydrogen bonds : angle 3.49668 ( 7038) covalent geometry : bond 0.00275 (34074) covalent geometry : angle 0.49615 (45970) *********************** 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 518 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 410 time to evaluate : 3.658 Fit side-chains REVERT: A 62 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7974 (mm-30) REVERT: A 157 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7616 (mtt-85) REVERT: B 62 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7873 (mm-30) REVERT: B 64 ARG cc_start: 0.8047 (tpt170) cc_final: 0.7542 (ttm170) REVERT: E 62 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7896 (mm-30) REVERT: F 62 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7924 (mm-30) REVERT: G 62 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7947 (mm-30) REVERT: H 62 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7917 (mm-30) REVERT: H 64 ARG cc_start: 0.8045 (tpt170) cc_final: 0.7568 (ttm170) REVERT: I 62 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7908 (mm-30) REVERT: L 62 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7908 (mm-30) REVERT: O 62 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7882 (mm-30) REVERT: P 62 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7925 (mm-30) REVERT: Q 62 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7951 (mm-30) REVERT: R 62 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7908 (mm-30) REVERT: S 62 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7930 (mm-30) REVERT: T 62 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7894 (mm-30) REVERT: U 62 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7905 (mm-30) REVERT: V 62 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7880 (mm-30) REVERT: W 62 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7909 (mm-30) REVERT: X 62 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7923 (mm-30) outliers start: 108 outliers final: 49 residues processed: 489 average time/residue: 1.7809 time to fit residues: 1005.8381 Evaluate side-chains 420 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 371 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 126 ASN Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 65 GLU Chi-restraints excluded: chain J residue 126 ASN Chi-restraints excluded: chain K residue 15 GLN Chi-restraints excluded: chain K residue 126 ASN Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 126 ASN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 126 ASN Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 126 ASN Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 126 ASN Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain T residue 15 GLN Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 126 ASN Chi-restraints excluded: chain V residue 15 GLN Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 126 ASN Chi-restraints excluded: chain X residue 126 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 267 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 364 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 395 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 309 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.120289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107343 restraints weight = 73572.161| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.87 r_work: 0.3097 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 34074 Z= 0.233 Angle : 0.617 8.668 45970 Z= 0.346 Chirality : 0.042 0.146 4858 Planarity : 0.003 0.027 6068 Dihedral : 4.233 21.312 4494 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.55 % Allowed : 12.80 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.13), residues: 4066 helix: 3.43 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -1.33 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP P 94 HIS 0.003 0.001 HIS D 58 PHE 0.010 0.002 PHE L 171 TYR 0.013 0.002 TYR B 33 ARG 0.003 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.12614 ( 2346) hydrogen bonds : angle 3.81021 ( 7038) covalent geometry : bond 0.00452 (34074) covalent geometry : angle 0.61726 (45970) *********************** 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 433 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 378 time to evaluate : 3.993 Fit side-chains REVERT: A 62 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8024 (mm-30) REVERT: B 62 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7956 (mm-30) REVERT: B 64 ARG cc_start: 0.8155 (tpt170) cc_final: 0.7621 (ttp-170) REVERT: E 62 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7958 (mm-30) REVERT: F 62 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8002 (mm-30) REVERT: G 62 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7994 (mm-30) REVERT: H 62 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7972 (mm-30) REVERT: H 64 ARG cc_start: 0.8167 (tpt170) cc_final: 0.7633 (ttp-170) REVERT: I 62 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7982 (mm-30) REVERT: L 62 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8000 (mm-30) REVERT: O 62 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7974 (mm-30) REVERT: P 62 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7978 (mm-30) REVERT: Q 62 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8003 (mm-30) REVERT: R 62 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7965 (mm-30) REVERT: S 62 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7997 (mm-30) REVERT: T 62 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7966 (mm-30) REVERT: U 62 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7987 (mm-30) REVERT: V 62 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7973 (mm-30) REVERT: W 62 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7983 (mm-30) REVERT: X 62 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7979 (mm-30) outliers start: 55 outliers final: 40 residues processed: 404 average time/residue: 2.0964 time to fit residues: 964.9903 Evaluate side-chains 393 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 353 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain I residue 126 ASN Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 126 ASN Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 126 ASN Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain M residue 126 ASN Chi-restraints excluded: chain N residue 126 ASN Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 126 ASN Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 126 ASN Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 126 ASN Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain W residue 126 ASN Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 126 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 36 optimal weight: 0.9990 chunk 301 optimal weight: 0.9990 chunk 233 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 365 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 350 optimal weight: 3.9990 chunk 309 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.126966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113680 restraints weight = 87421.292| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.04 r_work: 0.3211 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34074 Z= 0.172 Angle : 0.509 8.305 45970 Z= 0.290 Chirality : 0.038 0.133 4858 Planarity : 0.003 0.025 6068 Dihedral : 4.024 20.926 4494 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.69 % Allowed : 11.90 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.13), residues: 4066 helix: 3.77 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -1.13 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 94 HIS 0.003 0.001 HIS F 58 PHE 0.007 0.001 PHE M 171 TYR 0.010 0.001 TYR A 55 ARG 0.003 0.000 ARG K 64 Details of bonding type rmsd hydrogen bonds : bond 0.09787 ( 2346) hydrogen bonds : angle 3.54057 ( 7038) covalent geometry : bond 0.00284 (34074) covalent geometry : angle 0.50922 (45970) *********************** 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 477 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 382 time to evaluate : 3.680 Fit side-chains REVERT: A 62 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8042 (mm-30) REVERT: B 62 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7949 (mm-30) REVERT: B 64 ARG cc_start: 0.8139 (tpt170) cc_final: 0.7632 (ttm170) REVERT: E 62 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7953 (mm-30) REVERT: F 62 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8015 (mm-30) REVERT: G 62 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8012 (mm-30) REVERT: H 62 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8009 (mm-30) REVERT: H 64 ARG cc_start: 0.8191 (tpt170) cc_final: 0.7700 (ttm170) REVERT: I 62 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7974 (mm-30) REVERT: L 62 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8002 (mm-30) REVERT: O 62 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7991 (mm-30) REVERT: P 62 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7992 (mm-30) REVERT: Q 62 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8047 (mm-30) REVERT: R 62 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7984 (mm-30) REVERT: S 62 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8005 (mm-30) REVERT: T 62 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7966 (mm-30) REVERT: U 62 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7991 (mm-30) REVERT: V 62 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7980 (mm-30) REVERT: W 62 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8001 (mm-30) REVERT: X 62 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8011 (mm-30) outliers start: 95 outliers final: 64 residues processed: 448 average time/residue: 2.2183 time to fit residues: 1143.8711 Evaluate side-chains 443 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 379 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 126 ASN Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 126 ASN Chi-restraints excluded: chain K residue 15 GLN Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 126 ASN Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 126 ASN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 126 ASN Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 126 ASN Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 126 ASN Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain T residue 15 GLN Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 126 ASN Chi-restraints excluded: chain V residue 15 GLN Chi-restraints excluded: chain V residue 73 LEU Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 126 ASN Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 126 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 139 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 228 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.125575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112575 restraints weight = 77947.433| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.92 r_work: 0.3180 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1851 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= 0.182 Angle : 0.528 8.138 45970 Z= 0.300 Chirality : 0.038 0.137 4858 Planarity : 0.003 0.025 6068 Dihedral : 4.049 20.937 4494 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.35 % Allowed : 12.15 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.09 (0.13), residues: 4066 helix: 3.73 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -1.13 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP G 94 HIS 0.003 0.001 HIS Q 58 PHE 0.007 0.002 PHE C 171 TYR 0.010 0.001 TYR B 40 ARG 0.003 0.000 ARG S 64 Details of bonding type rmsd hydrogen bonds : bond 0.10369 ( 2346) hydrogen bonds : angle 3.58353 ( 7038) covalent geometry : bond 0.00312 (34074) covalent geometry : angle 0.52798 (45970) *********************** 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 487 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 404 time to evaluate : 3.770 Fit side-chains REVERT: A 62 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8002 (mm-30) REVERT: B 62 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7924 (mm-30) REVERT: B 64 ARG cc_start: 0.8144 (tpt170) cc_final: 0.7627 (ttm170) REVERT: E 62 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7934 (mm-30) REVERT: F 62 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7990 (mm-30) REVERT: G 62 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7969 (mm-30) REVERT: H 62 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7967 (mm-30) REVERT: H 64 ARG cc_start: 0.8154 (tpt170) cc_final: 0.7650 (ttm170) REVERT: I 62 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7953 (mm-30) REVERT: L 62 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7967 (mm-30) REVERT: O 62 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7962 (mm-30) REVERT: P 62 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7959 (mm-30) REVERT: Q 62 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7994 (mm-30) REVERT: R 62 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7938 (mm-30) REVERT: S 62 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7980 (mm-30) REVERT: T 62 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7934 (mm-30) REVERT: U 62 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7962 (mm-30) REVERT: V 62 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7950 (mm-30) REVERT: W 62 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7970 (mm-30) REVERT: X 62 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7972 (mm-30) outliers start: 83 outliers final: 72 residues processed: 442 average time/residue: 2.3051 time to fit residues: 1181.6025 Evaluate side-chains 473 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 401 time to evaluate : 4.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 126 ASN Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 126 ASN Chi-restraints excluded: chain K residue 15 GLN Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 126 ASN Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 126 ASN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 126 ASN Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 126 ASN Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 126 ASN Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain T residue 15 GLN Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 15 GLN Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 126 ASN Chi-restraints excluded: chain V residue 15 GLN Chi-restraints excluded: chain V residue 73 LEU Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 126 ASN Chi-restraints excluded: chain X residue 15 GLN Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 126 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 269 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 311 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 277 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.123149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109652 restraints weight = 89962.661| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.08 r_work: 0.3179 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 34074 Z= 0.202 Angle : 0.563 8.340 45970 Z= 0.318 Chirality : 0.040 0.142 4858 Planarity : 0.003 0.026 6068 Dihedral : 4.132 20.906 4494 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.20 % Allowed : 12.32 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.13), residues: 4066 helix: 3.62 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -1.21 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 94 HIS 0.003 0.001 HIS D 58 PHE 0.008 0.002 PHE C 171 TYR 0.011 0.002 TYR J 40 ARG 0.003 0.000 ARG W 64 Details of bonding type rmsd hydrogen bonds : bond 0.11343 ( 2346) hydrogen bonds : angle 3.68212 ( 7038) covalent geometry : bond 0.00366 (34074) covalent geometry : angle 0.56280 (45970) ********************** 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 476 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 398 time to evaluate : 4.156 Fit side-chains REVERT: A 15 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6236 (mm-40) REVERT: A 62 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8061 (mm-30) REVERT: B 62 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8016 (mm-30) REVERT: B 64 ARG cc_start: 0.8205 (tpt170) cc_final: 0.7691 (ttp-170) REVERT: C 15 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6159 (mm-40) REVERT: D 15 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6146 (mm-40) REVERT: E 62 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8010 (mm-30) REVERT: F 15 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6193 (mm-40) REVERT: F 62 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8051 (mm-30) REVERT: G 15 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6196 (mm-40) REVERT: G 62 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8033 (mm-30) REVERT: H 15 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6153 (mm-40) REVERT: H 62 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8048 (mm-30) REVERT: H 64 ARG cc_start: 0.8177 (tpt170) cc_final: 0.7666 (ttm170) REVERT: I 62 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8022 (mm-30) REVERT: L 62 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8048 (mm-30) REVERT: M 15 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6163 (mm-40) REVERT: N 15 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6199 (mm-40) REVERT: O 15 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6120 (mm-40) REVERT: O 62 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8020 (mm-30) REVERT: P 15 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6122 (mm-40) REVERT: P 62 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8023 (mm-30) REVERT: Q 15 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6228 (mm-40) REVERT: Q 62 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8054 (mm-30) REVERT: R 62 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8024 (mm-30) REVERT: S 15 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6131 (mm-40) REVERT: S 62 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8057 (mm-30) REVERT: T 62 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8013 (mm-30) REVERT: U 15 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6151 (mm-40) REVERT: U 62 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8042 (mm-30) REVERT: V 15 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6133 (mm-40) REVERT: V 62 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8020 (mm-30) REVERT: W 15 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6123 (mm-40) REVERT: W 62 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8028 (mm-30) REVERT: X 15 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6133 (mm-40) REVERT: X 62 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8034 (mm-30) outliers start: 78 outliers final: 49 residues processed: 431 average time/residue: 1.9691 time to fit residues: 973.5831 Evaluate side-chains 461 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 396 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain I residue 126 ASN Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 126 ASN Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 126 ASN Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 126 ASN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 126 ASN Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 126 ASN Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 126 ASN Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 15 GLN Chi-restraints excluded: chain U residue 73 LEU Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 126 ASN Chi-restraints excluded: chain V residue 15 GLN Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 126 ASN Chi-restraints excluded: chain X residue 15 GLN Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 126 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 127 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 301 optimal weight: 6.9990 chunk 355 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 278 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.125328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112492 restraints weight = 73076.371| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.86 r_work: 0.3217 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1840 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= 0.183 Angle : 0.529 8.225 45970 Z= 0.301 Chirality : 0.038 0.133 4858 Planarity : 0.003 0.025 6068 Dihedral : 4.051 20.592 4494 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.18 % Allowed : 12.41 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.13), residues: 4066 helix: 3.71 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -1.14 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I 94 HIS 0.003 0.001 HIS D 58 PHE 0.008 0.002 PHE M 171 TYR 0.011 0.002 TYR B 40 ARG 0.003 0.000 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.10363 ( 2346) hydrogen bonds : angle 3.58727 ( 7038) covalent geometry : bond 0.00312 (34074) covalent geometry : angle 0.52877 (45970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28984.37 seconds wall clock time: 508 minutes 6.59 seconds (30486.59 seconds total)