Starting phenix.real_space_refine on Tue Aug 26 13:01:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vd8_31910/08_2025/7vd8_31910.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vd8_31910/08_2025/7vd8_31910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vd8_31910/08_2025/7vd8_31910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vd8_31910/08_2025/7vd8_31910.map" model { file = "/net/cci-nas-00/data/ceres_data/7vd8_31910/08_2025/7vd8_31910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vd8_31910/08_2025/7vd8_31910.cif" } resolution = 1.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.615 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 254 6.06 5 S 192 5.16 5 Na 75 4.78 5 C 22248 2.51 5 N 6096 2.21 5 O 9336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38201 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "B" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "C" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "D" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "E" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "F" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "G" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "H" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "I" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "J" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "K" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "L" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "M" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "N" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "O" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "P" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "Q" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "R" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "S" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "T" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "U" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "V" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "W" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "X" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 3, ' ZN': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 3, ' ZN': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 3, ' ZN': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 3, ' ZN': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 4, ' ZN': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 4, ' ZN': 12} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 4, ' ZN': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 4, ' ZN': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "N" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "O" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 4, ' ZN': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "P" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' NA': 3, ' ZN': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "Q" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' NA': 3, ' ZN': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 2, ' ZN': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "T" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "U" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 2, ' ZN': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "V" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' NA': 3, ' ZN': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "W" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 2, ' ZN': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "X" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' NA': 2, ' ZN': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "E" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "F" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "G" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "H" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "J" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "K" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "M" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "O" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "P" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "Q" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "R" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "S" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "T" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "U" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "V" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "W" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "X" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Time building chain proxies: 18.51, per 1000 atoms: 0.48 Number of scatterers: 38201 At special positions: 0 Unit cell: (137.004, 137.004, 137.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 254 29.99 S 192 16.00 Na 75 11.00 O 9336 8.00 N 6096 7.00 C 22248 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: 3.13 Conformation dependent library (CDL) restraints added in 3.0 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 65 " pdb=" ZN A 214 " pdb="ZN ZN A 214 " - pdb=" NE2 HIS A 65 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 65 " pdb=" ZN B 214 " pdb="ZN ZN B 214 " - pdb=" NE2 HIS B 65 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 65 " pdb=" ZN C 214 " pdb="ZN ZN C 214 " - pdb=" NE2 HIS C 65 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" NE2 HIS D 65 " pdb=" ZN D 214 " pdb="ZN ZN D 214 " - pdb=" NE2 HIS D 65 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 65 " pdb=" ZN E 214 " pdb="ZN ZN E 214 " - pdb=" NE2 HIS E 65 " pdb=" ZN F 207 " pdb="ZN ZN F 207 " - pdb=" ND1 HIS F 65 " pdb=" ZN F 213 " pdb="ZN ZN F 213 " - pdb=" NE2 HIS F 65 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" ND1 HIS G 65 " pdb=" ZN G 214 " pdb="ZN ZN G 214 " - pdb=" NE2 HIS G 65 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 65 " pdb=" ZN H 213 " pdb="ZN ZN H 213 " - pdb=" NE2 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN I 214 " pdb="ZN ZN I 214 " - pdb=" NE2 HIS I 65 " pdb=" ZN J 208 " pdb="ZN ZN J 208 " - pdb=" NE2 HIS J 65 " pdb=" ZN J 213 " pdb="ZN ZN J 213 " - pdb=" NE2 HIS J 65 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 65 " pdb=" ZN K 214 " pdb="ZN ZN K 214 " - pdb=" NE2 HIS K 65 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 65 " pdb=" ZN L 214 " pdb="ZN ZN L 214 " - pdb=" NE2 HIS L 65 " pdb=" ZN M 204 " pdb="ZN ZN M 204 " - pdb=" ND1 HIS M 65 " pdb=" ZN M 213 " pdb="ZN ZN M 213 " - pdb=" NE2 HIS M 65 " pdb=" ZN N 207 " pdb="ZN ZN N 207 " - pdb=" ND1 HIS N 65 " pdb=" ZN N 212 " pdb="ZN ZN N 212 " - pdb=" NE2 HIS N 65 " pdb=" ZN O 204 " pdb="ZN ZN O 204 " - pdb=" ND1 HIS O 65 " pdb=" ZN O 214 " pdb="ZN ZN O 214 " - pdb=" NE2 HIS O 65 " pdb=" ZN P 207 " pdb="ZN ZN P 207 " - pdb=" ND1 HIS P 65 " pdb=" ZN P 211 " pdb="ZN ZN P 211 " - pdb=" NE2 HIS P 65 " pdb=" ZN Q 208 " pdb="ZN ZN Q 208 " - pdb=" ND1 HIS Q 65 " pdb=" ZN Q 212 " pdb="ZN ZN Q 212 " - pdb=" NE2 HIS Q 65 " pdb=" ZN R 209 " pdb="ZN ZN R 209 " - pdb=" ND1 HIS R 65 " pdb=" ZN R 213 " pdb="ZN ZN R 213 " - pdb=" NE2 HIS R 65 " pdb=" ZN S 207 " pdb="ZN ZN S 207 " - pdb=" ND1 HIS S 65 " pdb=" ZN S 211 " pdb="ZN ZN S 211 " - pdb=" NE2 HIS S 65 " pdb=" ZN T 208 " pdb="ZN ZN T 208 " - pdb=" ND1 HIS T 65 " pdb=" ZN T 213 " pdb="ZN ZN T 213 " - pdb=" NE2 HIS T 65 " pdb=" ZN U 207 " pdb="ZN ZN U 207 " - pdb=" ND1 HIS U 65 " pdb=" ZN U 211 " pdb="ZN ZN U 211 " - pdb=" NE2 HIS U 65 " pdb=" ZN V 208 " pdb="ZN ZN V 208 " - pdb=" ND1 HIS V 65 " pdb=" ZN V 212 " pdb="ZN ZN V 212 " - pdb=" NE2 HIS V 65 " pdb=" ZN W 207 " pdb="ZN ZN W 207 " - pdb=" ND1 HIS W 65 " pdb=" ZN W 211 " pdb="ZN ZN W 211 " - pdb=" NE2 HIS W 65 " pdb=" ZN X 207 " pdb="ZN ZN X 207 " - pdb=" ND1 HIS X 65 " pdb=" ZN X 212 " pdb="ZN ZN X 212 " - pdb=" NE2 HIS X 65 " 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8496 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 2688 hydrogen bonds defined for protein. 8064 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: 6.03 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11952 1.34 - 1.46: 5887 1.46 - 1.58: 17993 1.58 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 36120 Sorted by residual: bond pdb=" CB LYS E 86 " pdb=" CG LYS E 86 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" CB LYS N 86 " pdb=" CG LYS N 86 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CB LYS S 86 " pdb=" CG LYS S 86 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" CB LYS U 86 " pdb=" CG LYS U 86 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" CB LYS A 86 " pdb=" CG LYS A 86 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.42e+00 ... (remaining 36115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 47491 1.33 - 2.66: 859 2.66 - 3.99: 151 3.99 - 5.32: 79 5.32 - 6.65: 92 Bond angle restraints: 48672 Sorted by residual: angle pdb=" C TRP C 93 " pdb=" N GLU C 94 " pdb=" CA GLU C 94 " ideal model delta sigma weight residual 121.54 127.21 -5.67 1.91e+00 2.74e-01 8.80e+00 angle pdb=" C TRP J 93 " pdb=" N GLU J 94 " pdb=" CA GLU J 94 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.77e+00 angle pdb=" C TRP L 93 " pdb=" N GLU L 94 " pdb=" CA GLU L 94 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.75e+00 angle pdb=" C TRP W 93 " pdb=" N GLU W 94 " pdb=" CA GLU W 94 " ideal model delta sigma weight residual 121.54 127.18 -5.64 1.91e+00 2.74e-01 8.72e+00 angle pdb=" C TRP T 93 " pdb=" N GLU T 94 " pdb=" CA GLU T 94 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.66e+00 ... (remaining 48667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 19766 17.54 - 35.08: 1910 35.08 - 52.63: 501 52.63 - 70.17: 182 70.17 - 87.71: 57 Dihedral angle restraints: 22416 sinusoidal: 9576 harmonic: 12840 Sorted by residual: dihedral pdb=" CA TRP I 93 " pdb=" C TRP I 93 " pdb=" N GLU I 94 " pdb=" CA GLU I 94 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TRP M 93 " pdb=" C TRP M 93 " pdb=" N GLU M 94 " pdb=" CA GLU M 94 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TRP Q 93 " pdb=" C TRP Q 93 " pdb=" N GLU Q 94 " pdb=" CA GLU Q 94 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 22413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3582 0.028 - 0.056: 977 0.056 - 0.084: 408 0.084 - 0.112: 169 0.112 - 0.140: 48 Chirality restraints: 5184 Sorted by residual: chirality pdb=" CA TYR L 39 " pdb=" N TYR L 39 " pdb=" C TYR L 39 " pdb=" CB TYR L 39 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA TYR R 39 " pdb=" N TYR R 39 " pdb=" C TYR R 39 " pdb=" CB TYR R 39 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA TYR P 39 " pdb=" N TYR P 39 " pdb=" C TYR P 39 " pdb=" CB TYR P 39 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 5181 not shown) Planarity restraints: 6360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 63 " -0.116 9.50e-02 1.11e+02 5.25e-02 2.32e+00 pdb=" NE ARG P 63 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG P 63 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG P 63 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG P 63 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 63 " -0.114 9.50e-02 1.11e+02 5.16e-02 2.22e+00 pdb=" NE ARG U 63 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG U 63 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG U 63 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG U 63 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 63 " 0.113 9.50e-02 1.11e+02 5.11e-02 2.14e+00 pdb=" NE ARG Q 63 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG Q 63 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 63 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 63 " -0.000 2.00e-02 2.50e+03 ... (remaining 6357 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 1689 2.59 - 3.17: 33253 3.17 - 3.75: 76200 3.75 - 4.32: 99860 4.32 - 4.90: 157022 Nonbonded interactions: 368024 Sorted by model distance: nonbonded pdb=" OD1 ASP G 91 " pdb="ZN ZN G 206 " model vdw 2.013 2.230 nonbonded pdb=" OD1 ASP P 91 " pdb="ZN ZN P 202 " model vdw 2.013 2.230 nonbonded pdb=" OD1 ASP N 91 " pdb="ZN ZN N 203 " model vdw 2.013 2.230 nonbonded pdb=" OD1 ASP E 91 " pdb="ZN ZN E 204 " model vdw 2.022 2.230 nonbonded pdb=" OD1 ASP R 91 " pdb="ZN ZN R 205 " model vdw 2.022 2.230 ... (remaining 368019 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'B' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'C' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'D' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'E' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'F' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'G' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'H' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'I' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'J' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'K' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'L' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'M' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'N' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'O' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'P' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'Q' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'R' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'S' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'T' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'U' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'V' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'W' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'X' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) } 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=0.33 max=1.00 mean=0.96 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: 10.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 47.810 Find NCS groups from input model: 1.340 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:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.703 36168 Z= 0.572 Angle : 0.537 6.649 48672 Z= 0.288 Chirality : 0.035 0.140 5184 Planarity : 0.004 0.053 6360 Dihedral : 16.174 87.708 13920 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.03 % Allowed : 6.59 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.39 (0.13), residues: 4080 helix: 4.13 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.76 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 63 TYR 0.015 0.002 TYR B 39 PHE 0.011 0.002 PHE W 41 TRP 0.010 0.002 TRP M 93 HIS 0.003 0.001 HIS T 128 Details of bonding type rmsd covalent geometry : bond 0.00240 (36120) covalent geometry : angle 0.53737 (48672) hydrogen bonds : bond 0.05013 ( 2688) hydrogen bonds : angle 3.39892 ( 8064) metal coordination : bond 0.45890 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1021 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1021 average time/residue: 0.8921 time to fit residues: 1064.5126 Evaluate side-chains 975 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 975 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS A 139 ASN A 141 GLN B 13 HIS B 60 HIS B 139 ASN B 141 GLN C 13 HIS C 60 HIS C 139 ASN C 141 GLN D 60 HIS D 139 ASN D 141 GLN E 13 HIS E 60 HIS E 139 ASN E 141 GLN F 60 HIS F 141 GLN G 60 HIS G 105 HIS G 141 GLN H 60 HIS H 105 HIS H 139 ASN H 141 GLN I 13 HIS I 60 HIS I 141 GLN J 13 HIS J 60 HIS J 139 ASN J 141 GLN K 13 HIS K 60 HIS K 139 ASN K 141 GLN L 13 HIS L 60 HIS L 139 ASN L 141 GLN M 60 HIS M 105 HIS M 139 ASN M 141 GLN N 13 HIS N 60 HIS ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 ASN N 141 GLN O 60 HIS O 139 ASN O 141 GLN P 13 HIS P 60 HIS P 105 HIS P 141 GLN Q 13 HIS Q 60 HIS Q 141 GLN R 13 HIS R 60 HIS R 139 ASN R 141 GLN S 13 HIS S 60 HIS S 139 ASN S 141 GLN T 13 HIS T 139 ASN T 141 GLN U 13 HIS U 60 HIS U 139 ASN U 141 GLN V 60 HIS V 141 GLN W 13 HIS W 139 ASN X 13 HIS X 139 ASN X 141 GLN Total number of N/Q/H flips: 83 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.186590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.147269 restraints weight = 682316.660| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 5.66 r_work: 0.2717 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 36168 Z= 0.189 Angle : 0.637 6.810 48672 Z= 0.346 Chirality : 0.039 0.148 5184 Planarity : 0.006 0.058 6360 Dihedral : 4.508 21.378 4536 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.48 % Allowed : 6.11 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.97 (0.13), residues: 4080 helix: 3.82 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.69 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 63 TYR 0.019 0.003 TYR X 39 PHE 0.016 0.003 PHE C 41 TRP 0.005 0.002 TRP M 93 HIS 0.005 0.001 HIS O 128 Details of bonding type rmsd covalent geometry : bond 0.00381 (36120) covalent geometry : angle 0.63698 (48672) hydrogen bonds : bond 0.06306 ( 2688) hydrogen bonds : angle 3.81541 ( 8064) metal coordination : bond 0.00382 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 914 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 63 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7722 (tpp80) REVERT: E 116 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7672 (tp30) REVERT: F 116 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7703 (tp30) REVERT: G 63 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7743 (tpp80) REVERT: G 116 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7722 (tp30) REVERT: H 116 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7669 (tp30) REVERT: L 63 ARG cc_start: 0.7993 (tpp80) cc_final: 0.7626 (ttp-110) REVERT: M 86 LYS cc_start: 0.8178 (mmpt) cc_final: 0.7730 (mmpt) REVERT: M 116 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7696 (tp30) REVERT: O 63 ARG cc_start: 0.7862 (tpp80) cc_final: 0.7506 (ttp-110) REVERT: O 116 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7691 (tp30) REVERT: S 63 ARG cc_start: 0.7574 (ttp-170) cc_final: 0.7367 (ttp-110) REVERT: V 86 LYS cc_start: 0.8170 (mmpt) cc_final: 0.7581 (pttp) outliers start: 19 outliers final: 17 residues processed: 914 average time/residue: 0.8040 time to fit residues: 859.9192 Evaluate side-chains 913 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 896 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain K residue 90 CYS Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain O residue 90 CYS Chi-restraints excluded: chain P residue 90 CYS Chi-restraints excluded: chain Q residue 90 CYS Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain U residue 90 CYS Chi-restraints excluded: chain V residue 90 CYS Chi-restraints excluded: chain W residue 90 CYS Chi-restraints excluded: chain X residue 90 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 258 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 386 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 316 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 272 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS A 65 HIS B 13 HIS B 60 HIS C 13 HIS C 60 HIS D 60 HIS E 13 HIS E 60 HIS G 60 HIS G 105 HIS H 60 HIS I 13 HIS I 60 HIS J 13 HIS K 13 HIS K 60 HIS K 65 HIS L 13 HIS L 60 HIS M 60 HIS N 13 HIS N 60 HIS N 105 HIS O 60 HIS P 13 HIS P 105 HIS Q 13 HIS R 13 HIS S 13 HIS S 60 HIS T 13 HIS U 13 HIS V 60 HIS W 13 HIS W 141 GLN X 13 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.187823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.150094 restraints weight = 704726.756| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 5.43 r_work: 0.2758 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.630 36168 Z= 0.217 Angle : 0.571 6.236 48672 Z= 0.308 Chirality : 0.037 0.143 5184 Planarity : 0.004 0.031 6360 Dihedral : 4.413 21.313 4536 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.53 % Allowed : 6.31 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.16 (0.13), residues: 4080 helix: 3.95 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.75 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 63 TYR 0.017 0.002 TYR W 39 PHE 0.013 0.002 PHE E 41 TRP 0.007 0.002 TRP K 93 HIS 0.003 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00284 (36120) covalent geometry : angle 0.57074 (48672) hydrogen bonds : bond 0.05639 ( 2688) hydrogen bonds : angle 3.62596 ( 8064) metal coordination : bond 0.13070 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 930 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7709 (tp30) REVERT: C 116 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7684 (tp30) REVERT: G 86 LYS cc_start: 0.8108 (mmpt) cc_final: 0.7580 (pttp) REVERT: H 116 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7692 (tp30) REVERT: O 63 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7574 (ttp-110) REVERT: W 116 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7724 (tp30) outliers start: 21 outliers final: 17 residues processed: 930 average time/residue: 0.9217 time to fit residues: 999.0155 Evaluate side-chains 925 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 908 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain K residue 90 CYS Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain O residue 90 CYS Chi-restraints excluded: chain P residue 90 CYS Chi-restraints excluded: chain Q residue 90 CYS Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain T residue 90 CYS Chi-restraints excluded: chain U residue 90 CYS Chi-restraints excluded: chain W residue 90 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 361 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 373 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 350 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS B 13 HIS B 60 HIS B 141 GLN C 13 HIS C 60 HIS C 141 GLN D 60 HIS E 13 HIS E 60 HIS E 105 HIS F 141 GLN G 60 HIS G 105 HIS G 141 GLN H 60 HIS ** H 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 GLN I 13 HIS I 60 HIS J 13 HIS K 13 HIS K 60 HIS K 141 GLN L 13 HIS L 60 HIS L 141 GLN M 60 HIS M 141 GLN N 13 HIS O 60 HIS O 141 GLN P 13 HIS P 105 HIS P 141 GLN Q 13 HIS R 13 HIS R 141 GLN S 13 HIS S 141 GLN T 13 HIS U 13 HIS U 141 GLN V 60 HIS V 141 GLN W 13 HIS X 13 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.185889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.146884 restraints weight = 700359.845| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 6.27 r_work: 0.2708 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 36168 Z= 0.199 Angle : 0.653 6.998 48672 Z= 0.356 Chirality : 0.040 0.150 5184 Planarity : 0.006 0.059 6360 Dihedral : 4.563 21.328 4536 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.61 % Allowed : 7.63 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.78 (0.13), residues: 4080 helix: 3.69 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.63 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 63 TYR 0.018 0.003 TYR M 39 PHE 0.017 0.003 PHE Q 41 TRP 0.005 0.002 TRP V 93 HIS 0.006 0.002 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00404 (36120) covalent geometry : angle 0.65306 (48672) hydrogen bonds : bond 0.06504 ( 2688) hydrogen bonds : angle 3.89324 ( 8064) metal coordination : bond 0.00530 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 907 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7685 (tp30) REVERT: E 116 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7717 (tp30) REVERT: H 116 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7680 (tp30) REVERT: M 116 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7688 (tp30) REVERT: O 63 ARG cc_start: 0.7933 (tpp80) cc_final: 0.7569 (ttp-110) REVERT: W 116 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7660 (tp30) outliers start: 24 outliers final: 22 residues processed: 908 average time/residue: 0.9332 time to fit residues: 988.5473 Evaluate side-chains 908 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 886 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain K residue 90 CYS Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain O residue 90 CYS Chi-restraints excluded: chain P residue 90 CYS Chi-restraints excluded: chain Q residue 90 CYS Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain T residue 90 CYS Chi-restraints excluded: chain U residue 90 CYS Chi-restraints excluded: chain V residue 90 CYS Chi-restraints excluded: chain W residue 90 CYS Chi-restraints excluded: chain X residue 90 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 51 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 312 optimal weight: 0.5980 chunk 327 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 282 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS A 141 GLN B 13 HIS B 60 HIS C 13 HIS C 60 HIS D 60 HIS D 141 GLN E 13 HIS E 60 HIS E 141 GLN G 60 HIS G 105 HIS H 60 HIS I 13 HIS I 60 HIS I 141 GLN J 13 HIS J 141 GLN K 13 HIS K 60 HIS L 13 HIS L 60 HIS M 60 HIS M 105 HIS N 13 HIS N 105 HIS N 141 GLN O 60 HIS P 13 HIS P 105 HIS Q 13 HIS Q 141 GLN R 13 HIS S 13 HIS T 13 HIS T 141 GLN U 13 HIS V 60 HIS W 13 HIS W 125 ASN W 141 GLN X 13 HIS X 141 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.187872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.149262 restraints weight = 703631.552| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 6.28 r_work: 0.2753 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36168 Z= 0.152 Angle : 0.579 6.306 48672 Z= 0.313 Chirality : 0.037 0.144 5184 Planarity : 0.004 0.033 6360 Dihedral : 4.440 21.165 4536 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.53 % Allowed : 8.23 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.10 (0.13), residues: 4080 helix: 3.91 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.73 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 63 TYR 0.017 0.002 TYR W 39 PHE 0.014 0.003 PHE C 41 TRP 0.007 0.002 TRP V 93 HIS 0.004 0.001 HIS R 128 Details of bonding type rmsd covalent geometry : bond 0.00292 (36120) covalent geometry : angle 0.57920 (48672) hydrogen bonds : bond 0.05734 ( 2688) hydrogen bonds : angle 3.67097 ( 8064) metal coordination : bond 0.00337 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 927 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7709 (tp30) REVERT: C 116 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7675 (tp30) REVERT: H 116 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7684 (tp30) REVERT: M 116 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7676 (tp30) REVERT: O 63 ARG cc_start: 0.7870 (tpp80) cc_final: 0.7558 (ttp-110) REVERT: W 116 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7704 (tp30) outliers start: 21 outliers final: 21 residues processed: 927 average time/residue: 0.8339 time to fit residues: 902.1556 Evaluate side-chains 906 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 885 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain K residue 90 CYS Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain O residue 90 CYS Chi-restraints excluded: chain P residue 90 CYS Chi-restraints excluded: chain Q residue 90 CYS Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain T residue 90 CYS Chi-restraints excluded: chain U residue 90 CYS Chi-restraints excluded: chain V residue 90 CYS Chi-restraints excluded: chain W residue 90 CYS Chi-restraints excluded: chain X residue 90 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 133 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 368 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 363 optimal weight: 5.9990 chunk 401 optimal weight: 0.9980 chunk 342 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS B 13 HIS B 60 HIS C 13 HIS C 60 HIS C 141 GLN D 60 HIS E 13 HIS E 60 HIS G 60 HIS G 105 HIS G 141 GLN H 60 HIS H 105 HIS H 141 GLN I 13 HIS I 60 HIS J 13 HIS K 13 HIS K 60 HIS L 13 HIS L 60 HIS L 141 GLN M 60 HIS M 105 HIS N 13 HIS O 60 HIS P 13 HIS P 105 HIS P 141 GLN Q 13 HIS R 13 HIS S 13 HIS T 13 HIS U 13 HIS U 141 GLN V 60 HIS V 141 GLN W 13 HIS X 13 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.187244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.148845 restraints weight = 715654.965| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 6.42 r_work: 0.2746 rms_B_bonded: 5.34 restraints_weight: 2.0000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36168 Z= 0.162 Angle : 0.599 6.457 48672 Z= 0.325 Chirality : 0.038 0.146 5184 Planarity : 0.004 0.037 6360 Dihedral : 4.468 21.214 4536 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.58 % Allowed : 8.61 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.01 (0.13), residues: 4080 helix: 3.85 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.71 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 63 TYR 0.017 0.002 TYR W 39 PHE 0.015 0.003 PHE Q 41 TRP 0.006 0.002 TRP U 93 HIS 0.004 0.001 HIS M 105 Details of bonding type rmsd covalent geometry : bond 0.00315 (36120) covalent geometry : angle 0.59909 (48672) hydrogen bonds : bond 0.05920 ( 2688) hydrogen bonds : angle 3.72355 ( 8064) metal coordination : bond 0.00399 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 906 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7708 (tp30) REVERT: F 116 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7710 (tp30) REVERT: H 116 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7697 (tp30) REVERT: M 116 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7672 (tp30) REVERT: N 116 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7688 (tp30) REVERT: O 63 ARG cc_start: 0.7901 (tpp80) cc_final: 0.7567 (ttp-110) REVERT: P 86 LYS cc_start: 0.8172 (mmpt) cc_final: 0.7634 (pttp) REVERT: W 116 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7696 (tp30) outliers start: 23 outliers final: 22 residues processed: 906 average time/residue: 0.8308 time to fit residues: 881.1710 Evaluate side-chains 883 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 861 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain K residue 90 CYS Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain O residue 90 CYS Chi-restraints excluded: chain P residue 90 CYS Chi-restraints excluded: chain Q residue 90 CYS Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain T residue 90 CYS Chi-restraints excluded: chain U residue 90 CYS Chi-restraints excluded: chain V residue 90 CYS Chi-restraints excluded: chain W residue 90 CYS Chi-restraints excluded: chain X residue 90 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 0 optimal weight: 10.0000 chunk 313 optimal weight: 0.6980 chunk 252 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 373 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 360 optimal weight: 8.9990 chunk 32 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS A 141 GLN B 13 HIS B 60 HIS B 141 GLN C 13 HIS C 60 HIS D 60 HIS D 141 GLN E 13 HIS E 60 HIS E 105 HIS G 60 HIS G 105 HIS H 60 HIS I 13 HIS I 60 HIS J 13 HIS J 141 GLN K 13 HIS K 60 HIS L 13 HIS L 60 HIS M 60 HIS M 105 HIS N 13 HIS N 105 HIS O 60 HIS P 13 HIS P 105 HIS Q 13 HIS R 13 HIS S 13 HIS T 13 HIS U 13 HIS V 60 HIS W 13 HIS W 141 GLN X 13 HIS X 141 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.188444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.149269 restraints weight = 702505.587| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 6.12 r_work: 0.2758 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36168 Z= 0.153 Angle : 0.585 6.523 48672 Z= 0.317 Chirality : 0.037 0.145 5184 Planarity : 0.004 0.032 6360 Dihedral : 4.440 21.194 4536 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.61 % Allowed : 8.74 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.09 (0.13), residues: 4080 helix: 3.91 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.73 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 63 TYR 0.017 0.002 TYR W 39 PHE 0.014 0.003 PHE Q 41 TRP 0.007 0.002 TRP V 93 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00294 (36120) covalent geometry : angle 0.58539 (48672) hydrogen bonds : bond 0.05729 ( 2688) hydrogen bonds : angle 3.67223 ( 8064) metal coordination : bond 0.00348 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 885 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7713 (tp30) REVERT: C 116 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7674 (tp30) REVERT: E 116 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7727 (tp30) REVERT: G 116 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7741 (tp30) REVERT: H 116 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7693 (tp30) REVERT: M 116 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7673 (tp30) REVERT: N 116 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7708 (tp30) REVERT: O 63 ARG cc_start: 0.7887 (tpp80) cc_final: 0.7563 (ttp-110) REVERT: P 86 LYS cc_start: 0.8168 (mmpt) cc_final: 0.7625 (pttp) REVERT: U 116 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7682 (tp30) REVERT: W 116 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7684 (tp30) outliers start: 24 outliers final: 24 residues processed: 885 average time/residue: 0.9240 time to fit residues: 954.4725 Evaluate side-chains 875 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 851 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 90 CYS Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain K residue 90 CYS Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain N residue 90 CYS Chi-restraints excluded: chain O residue 90 CYS Chi-restraints excluded: chain P residue 90 CYS Chi-restraints excluded: chain Q residue 90 CYS Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain T residue 90 CYS Chi-restraints excluded: chain U residue 90 CYS Chi-restraints excluded: chain V residue 90 CYS Chi-restraints excluded: chain W residue 90 CYS Chi-restraints excluded: chain X residue 90 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 113 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 278 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 260 optimal weight: 0.9990 chunk 250 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS B 13 HIS B 60 HIS C 13 HIS C 60 HIS D 60 HIS E 13 HIS E 60 HIS G 60 HIS G 105 HIS H 60 HIS H 141 GLN I 13 HIS I 60 HIS J 13 HIS K 13 HIS K 60 HIS L 13 HIS L 60 HIS M 60 HIS M 105 HIS N 13 HIS O 60 HIS P 13 HIS P 105 HIS Q 13 HIS R 13 HIS S 13 HIS T 13 HIS U 13 HIS V 60 HIS W 13 HIS X 13 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.188005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.149583 restraints weight = 746511.867| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 6.53 r_work: 0.2751 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36168 Z= 0.147 Angle : 0.576 6.398 48672 Z= 0.312 Chirality : 0.037 0.144 5184 Planarity : 0.004 0.028 6360 Dihedral : 4.417 21.260 4536 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.58 % Allowed : 8.76 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.14 (0.13), residues: 4080 helix: 3.94 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.73 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 63 TYR 0.017 0.002 TYR B 39 PHE 0.013 0.002 PHE Q 41 TRP 0.007 0.002 TRP V 93 HIS 0.003 0.001 HIS S 128 Details of bonding type rmsd covalent geometry : bond 0.00281 (36120) covalent geometry : angle 0.57593 (48672) hydrogen bonds : bond 0.05589 ( 2688) hydrogen bonds : angle 3.63626 ( 8064) metal coordination : bond 0.00315 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 897 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7715 (tp30) REVERT: C 116 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7688 (tp30) REVERT: E 116 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7737 (tp30) REVERT: F 116 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7728 (tp30) REVERT: G 116 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7725 (tp30) REVERT: H 116 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7710 (tp30) REVERT: M 116 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7674 (tp30) REVERT: N 116 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7698 (tp30) REVERT: O 63 ARG cc_start: 0.7875 (tpp80) cc_final: 0.7576 (ttp-110) REVERT: P 86 LYS cc_start: 0.8168 (mmpt) cc_final: 0.7592 (pttp) REVERT: U 116 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7687 (tp30) REVERT: W 116 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7691 (tp30) outliers start: 23 outliers final: 22 residues processed: 897 average time/residue: 0.9591 time to fit residues: 1004.4280 Evaluate side-chains 885 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 863 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 90 CYS Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain K residue 90 CYS Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain N residue 90 CYS Chi-restraints excluded: chain O residue 90 CYS Chi-restraints excluded: chain P residue 90 CYS Chi-restraints excluded: chain Q residue 90 CYS Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain T residue 90 CYS Chi-restraints excluded: chain U residue 90 CYS Chi-restraints excluded: chain V residue 90 CYS Chi-restraints excluded: chain X residue 90 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 154 optimal weight: 2.9990 chunk 282 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 361 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 280 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 276 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 308 optimal weight: 5.9990 chunk 300 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS A 141 GLN B 13 HIS B 60 HIS B 141 GLN C 13 HIS C 60 HIS C 141 GLN D 60 HIS D 141 GLN E 13 HIS E 60 HIS G 60 HIS G 105 HIS G 141 GLN H 60 HIS I 13 HIS I 60 HIS J 13 HIS J 141 GLN K 13 HIS K 60 HIS L 13 HIS L 60 HIS M 60 HIS M 105 HIS N 13 HIS O 60 HIS P 13 HIS P 105 HIS P 141 GLN Q 13 HIS R 13 HIS S 13 HIS T 13 HIS U 13 HIS V 60 HIS W 13 HIS W 141 GLN X 13 HIS X 141 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.188823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.149754 restraints weight = 700744.539| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 6.08 r_work: 0.2771 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36168 Z= 0.146 Angle : 0.575 6.604 48672 Z= 0.311 Chirality : 0.037 0.144 5184 Planarity : 0.004 0.027 6360 Dihedral : 4.419 21.298 4536 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.61 % Allowed : 8.76 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.14 (0.13), residues: 4080 helix: 3.94 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.73 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 63 TYR 0.017 0.002 TYR C 39 PHE 0.013 0.002 PHE Q 41 TRP 0.007 0.002 TRP S 93 HIS 0.003 0.001 HIS H 128 Details of bonding type rmsd covalent geometry : bond 0.00278 (36120) covalent geometry : angle 0.57457 (48672) hydrogen bonds : bond 0.05561 ( 2688) hydrogen bonds : angle 3.63303 ( 8064) metal coordination : bond 0.00309 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 872 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7708 (tp30) REVERT: E 116 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7719 (tp30) REVERT: F 116 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7718 (tp30) REVERT: G 116 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7709 (tp30) REVERT: H 116 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7688 (tp30) REVERT: M 116 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7677 (tp30) REVERT: N 116 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7715 (tp30) REVERT: O 63 ARG cc_start: 0.7864 (tpp80) cc_final: 0.7578 (ttp-110) REVERT: P 86 LYS cc_start: 0.8157 (mmpt) cc_final: 0.7595 (pttp) REVERT: W 116 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7686 (tp30) outliers start: 24 outliers final: 24 residues processed: 872 average time/residue: 0.9704 time to fit residues: 989.6141 Evaluate side-chains 865 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 841 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 90 CYS Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain K residue 90 CYS Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain N residue 90 CYS Chi-restraints excluded: chain O residue 90 CYS Chi-restraints excluded: chain P residue 90 CYS Chi-restraints excluded: chain Q residue 90 CYS Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain T residue 90 CYS Chi-restraints excluded: chain U residue 90 CYS Chi-restraints excluded: chain V residue 90 CYS Chi-restraints excluded: chain W residue 90 CYS Chi-restraints excluded: chain X residue 90 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 147 optimal weight: 0.4980 chunk 227 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 305 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 162 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS B 13 HIS B 60 HIS C 13 HIS C 60 HIS D 60 HIS E 13 HIS E 60 HIS G 60 HIS G 105 HIS H 60 HIS H 141 GLN I 13 HIS I 60 HIS J 13 HIS K 13 HIS K 60 HIS L 13 HIS L 60 HIS L 141 GLN M 60 HIS M 105 HIS N 13 HIS O 60 HIS P 13 HIS P 105 HIS Q 13 HIS R 13 HIS S 13 HIS T 13 HIS U 13 HIS V 60 HIS W 13 HIS X 13 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.188560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.150071 restraints weight = 689103.123| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 6.23 r_work: 0.2760 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36168 Z= 0.148 Angle : 0.580 6.553 48672 Z= 0.314 Chirality : 0.037 0.144 5184 Planarity : 0.004 0.029 6360 Dihedral : 4.421 21.332 4536 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.61 % Allowed : 8.86 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.11 (0.13), residues: 4080 helix: 3.92 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.73 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 63 TYR 0.017 0.002 TYR W 39 PHE 0.014 0.002 PHE Q 41 TRP 0.007 0.002 TRP I 93 HIS 0.004 0.001 HIS S 128 Details of bonding type rmsd covalent geometry : bond 0.00282 (36120) covalent geometry : angle 0.57980 (48672) hydrogen bonds : bond 0.05581 ( 2688) hydrogen bonds : angle 3.63994 ( 8064) metal coordination : bond 0.00316 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 868 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7722 (tp30) REVERT: E 116 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7712 (tp30) REVERT: F 116 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7709 (tp30) REVERT: H 116 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7689 (tp30) REVERT: M 116 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7677 (tp30) REVERT: N 116 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7690 (tp30) REVERT: O 63 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7569 (ttp-110) REVERT: P 86 LYS cc_start: 0.8159 (mmpt) cc_final: 0.7590 (pttp) REVERT: W 116 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7689 (tp30) outliers start: 24 outliers final: 24 residues processed: 868 average time/residue: 0.8174 time to fit residues: 831.7158 Evaluate side-chains 884 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 860 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 90 CYS Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain K residue 90 CYS Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain M residue 90 CYS Chi-restraints excluded: chain N residue 90 CYS Chi-restraints excluded: chain O residue 90 CYS Chi-restraints excluded: chain P residue 90 CYS Chi-restraints excluded: chain Q residue 90 CYS Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain S residue 90 CYS Chi-restraints excluded: chain T residue 90 CYS Chi-restraints excluded: chain U residue 90 CYS Chi-restraints excluded: chain V residue 90 CYS Chi-restraints excluded: chain W residue 90 CYS Chi-restraints excluded: chain X residue 90 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 95 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 313 optimal weight: 0.9990 chunk 336 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 243 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 347 optimal weight: 0.2980 chunk 387 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS A 141 GLN B 13 HIS B 60 HIS B 141 GLN C 13 HIS C 60 HIS C 141 GLN D 60 HIS D 141 GLN E 13 HIS E 60 HIS G 60 HIS G 105 HIS G 141 GLN H 60 HIS I 13 HIS I 60 HIS J 13 HIS J 141 GLN K 13 HIS K 60 HIS K 141 GLN L 13 HIS L 60 HIS M 60 HIS M 105 HIS N 13 HIS N 141 GLN O 60 HIS P 13 HIS P 105 HIS P 141 GLN Q 13 HIS R 13 HIS S 13 HIS T 13 HIS U 13 HIS U 141 GLN V 60 HIS W 13 HIS W 141 GLN X 13 HIS X 141 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.188177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.150639 restraints weight = 751420.326| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 6.10 r_work: 0.2768 rms_B_bonded: 5.26 restraints_weight: 2.0000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36168 Z= 0.145 Angle : 0.575 6.546 48672 Z= 0.312 Chirality : 0.037 0.143 5184 Planarity : 0.004 0.027 6360 Dihedral : 4.418 21.376 4536 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.61 % Allowed : 8.86 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.13 (0.13), residues: 4080 helix: 3.93 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.73 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 63 TYR 0.017 0.002 TYR C 39 PHE 0.013 0.002 PHE P 41 TRP 0.007 0.002 TRP S 93 HIS 0.003 0.001 HIS S 128 Details of bonding type rmsd covalent geometry : bond 0.00277 (36120) covalent geometry : angle 0.57518 (48672) hydrogen bonds : bond 0.05526 ( 2688) hydrogen bonds : angle 3.62773 ( 8064) metal coordination : bond 0.00301 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21653.36 seconds wall clock time: 369 minutes 8.48 seconds (22148.48 seconds total)