Starting phenix.real_space_refine on Wed Aug 5 17:10:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10se_75432/08_2026/10se_75432.cif Found real_map, /net/cci-nas-00/data/ceres_data/10se_75432/08_2026/10se_75432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10se_75432/08_2026/10se_75432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10se_75432/08_2026/10se_75432.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10se_75432/08_2026/10se_75432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10se_75432/08_2026/10se_75432.map" } resolution = 2.41 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= 0.002 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: 3 Type Number sf(0) Gaussians C 7308 2.51 5 N 1764 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10710 Number of models: 1 Model: "" Number of chains: 378 Chain: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AC" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AE" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AF" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AG" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AI" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AC" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AD" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AE" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AF" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AG" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AH" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AI" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AJ" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AK" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AM" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AO" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AQ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AS" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AS" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AT" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AU" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AV" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AW" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AX" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AY" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AY" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AZ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AZ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AK" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AL" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AN" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AO" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AP" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AQ" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AR" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AS" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AT" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AU" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AV" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AW" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AX" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AY" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AZ" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A0" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A1" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A2" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A3" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A4" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A5" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A6" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A7" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A8" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A9" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BC" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BD" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BE" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BF" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BG" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BH" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BI" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BJ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A2" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A3" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A4" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A5" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A6" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A7" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A8" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A9" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BB" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BC" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BD" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BE" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BF" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BG" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BH" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BI" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BJ" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BK" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BL" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BM" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BN" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BO" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BP" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BQ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BR" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BS" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BS" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BT" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BU" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BV" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BW" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BX" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BY" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BY" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BZ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BZ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BK" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BL" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BM" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BN" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BO" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BP" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BQ" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BR" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BS" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BT" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BU" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BV" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BW" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BX" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BY" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BZ" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B0" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B1" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.59, per 1000 atoms: 0.24 Number of scatterers: 10710 At special positions: 0 Unit cell: (103.8, 117.64, 64.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1638 8.00 N 1764 7.00 C 7308 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=258, symmetry=0 Number of additional bonds: simple=258, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 327.3 milliseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... No hydrogen bonds 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: 0.01 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 1386 1.28 - 1.35: 1360 1.35 - 1.42: 1411 1.42 - 1.50: 1809 1.50 - 1.57: 4744 Bond restraints: 10710 Sorted by residual: bond pdb=" CA SER s 10 " pdb=" CB SER s 10 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.34e-02 5.57e+03 1.38e+01 bond pdb=" CA SER E 10 " pdb=" CB SER E 10 " ideal model delta sigma weight residual 1.529 1.479 0.049 1.34e-02 5.57e+03 1.36e+01 bond pdb=" CA SER S 10 " pdb=" CB SER S 10 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.34e-02 5.57e+03 1.35e+01 bond pdb=" CA SERA2 10 " pdb=" CB SERA2 10 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.34e-02 5.57e+03 1.33e+01 bond pdb=" CA SERAK 10 " pdb=" CB SERAK 10 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.34e-02 5.57e+03 1.33e+01 ... (remaining 10705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 10947 2.02 - 4.04: 2420 4.04 - 6.07: 362 6.07 - 8.09: 82 8.09 - 10.11: 49 Bond angle restraints: 13860 Sorted by residual: angle pdb=" N TYRBX 3 " pdb=" CA TYRBX 3 " pdb=" CB TYRBX 3 " ideal model delta sigma weight residual 110.79 120.25 -9.46 1.30e+00 5.92e-01 5.30e+01 angle pdb=" N TYRAX 3 " pdb=" CA TYRAX 3 " pdb=" CB TYRAX 3 " ideal model delta sigma weight residual 110.79 120.24 -9.45 1.30e+00 5.92e-01 5.28e+01 angle pdb=" N TYR 5 3 " pdb=" CA TYR 5 3 " pdb=" CB TYR 5 3 " ideal model delta sigma weight residual 110.79 120.23 -9.44 1.30e+00 5.92e-01 5.27e+01 angle pdb=" N TYRAF 3 " pdb=" CA TYRAF 3 " pdb=" CB TYRAF 3 " ideal model delta sigma weight residual 110.79 120.23 -9.44 1.30e+00 5.92e-01 5.27e+01 angle pdb=" N TYR P 3 " pdb=" CA TYR P 3 " pdb=" CB TYR P 3 " ideal model delta sigma weight residual 110.79 120.21 -9.42 1.30e+00 5.92e-01 5.25e+01 ... (remaining 13855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.20: 5530 14.20 - 28.41: 521 28.41 - 42.61: 95 42.61 - 56.81: 14 56.81 - 71.01: 14 Dihedral angle restraints: 6174 sinusoidal: 2898 harmonic: 3276 Sorted by residual: dihedral pdb=" CA SERAK 10 " pdb=" C SERAK 10 " pdb=" N LYSAK 11 " pdb=" CA LYSAK 11 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA SERBK 10 " pdb=" C SERBK 10 " pdb=" N LYSBK 11 " pdb=" CA LYSBK 11 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA SER s 10 " pdb=" C SER s 10 " pdb=" N LYS s 11 " pdb=" CA LYS s 11 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 6171 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.070: 701 0.070 - 0.140: 484 0.140 - 0.209: 152 0.209 - 0.279: 42 0.279 - 0.348: 7 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA PRO c 4 " pdb=" N PRO c 4 " pdb=" C PRO c 4 " pdb=" CB PRO c 4 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA PROA4 4 " pdb=" N PROA4 4 " pdb=" C PROA4 4 " pdb=" CB PROA4 4 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA PRO U 4 " pdb=" N PRO U 4 " pdb=" C PRO U 4 " pdb=" CB PRO U 4 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 1383 not shown) Planarity restraints: 1512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRBK 3 " -0.052 2.00e-02 2.50e+03 3.11e-02 1.94e+01 pdb=" CG TYRBK 3 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYRBK 3 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYRBK 3 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYRBK 3 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYRBK 3 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYRBK 3 " -0.027 2.00e-02 2.50e+03 pdb=" OH TYRBK 3 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRA2 3 " -0.052 2.00e-02 2.50e+03 3.11e-02 1.94e+01 pdb=" CG TYRA2 3 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYRA2 3 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYRA2 3 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYRA2 3 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYRA2 3 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYRA2 3 " -0.027 2.00e-02 2.50e+03 pdb=" OH TYRA2 3 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR s 3 " -0.052 2.00e-02 2.50e+03 3.11e-02 1.94e+01 pdb=" CG TYR s 3 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR s 3 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR s 3 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR s 3 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR s 3 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR s 3 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR s 3 " -0.034 2.00e-02 2.50e+03 ... (remaining 1509 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 3076 2.88 - 3.39: 8479 3.39 - 3.89: 18728 3.89 - 4.40: 22886 4.40 - 4.90: 41993 Nonbonded interactions: 95162 Sorted by model distance: nonbonded pdb=" OH TYRAM 3 " pdb=" ND1 HISA2 2 " model vdw 2.380 3.120 nonbonded pdb=" ND1 HIS E 2 " pdb=" OH TYR c 3 " model vdw 2.380 3.120 nonbonded pdb=" OH TYR u 3 " pdb=" ND1 HISAK 2 " model vdw 2.380 3.120 nonbonded pdb=" OH TYRA4 3 " pdb=" ND1 HISBK 2 " model vdw 2.380 3.120 nonbonded pdb=" OH TYR B 3 " pdb=" ND1 HIS s 2 " model vdw 2.380 3.120 ... (remaining 95157 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'A0' selection = chain 'A1' selection = chain 'A2' selection = chain 'A3' selection = chain 'A4' selection = chain 'A5' selection = chain 'A6' selection = chain 'A7' selection = chain 'A8' selection = chain 'A9' selection = chain 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'AE' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'AI' selection = chain 'AJ' selection = chain 'AK' selection = chain 'AL' selection = chain 'AM' selection = chain 'AN' selection = chain 'AO' selection = chain 'AP' selection = chain 'AQ' selection = chain 'AR' selection = chain 'AS' selection = chain 'AT' selection = chain 'AU' selection = chain 'AV' selection = chain 'AW' selection = chain 'AX' selection = chain 'AY' selection = chain 'AZ' selection = chain 'B' selection = chain 'B0' selection = chain 'B1' selection = chain 'BA' selection = chain 'BB' selection = chain 'BC' selection = chain 'BD' selection = chain 'BE' selection = chain 'BF' selection = chain 'BG' selection = chain 'BH' selection = chain 'BI' selection = chain 'BJ' selection = chain 'BK' selection = chain 'BL' selection = chain 'BM' selection = chain 'BN' selection = chain 'BO' selection = chain 'BP' selection = chain 'BQ' selection = chain 'BR' selection = chain 'BS' selection = chain 'BT' selection = chain 'BU' selection = chain 'BV' selection = chain 'BW' selection = chain 'BX' selection = chain 'BY' selection = chain 'BZ' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.020 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.030 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.110 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:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 0.025 0.190 10968 Z= 2.262 Angle : 1.835 10.112 13860 Z= 1.098 Chirality : 0.100 0.348 1386 Planarity : 0.010 0.035 1512 Dihedral : 11.479 71.012 4158 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.28 % Favored : 84.72 % Rotamer: Outliers : 2.78 % Allowed : 3.47 % Favored : 93.75 % Cbeta Deviations : 0.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.22), residues: 1008 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.052 0.010 TYRBK 3 HIS 0.031 0.004 HISAW 2 Details of bonding type rmsd/Z covalent geometry : bond 0.01273 / 0.78 (10710) covalent geometry : angle 1.83525 / 1.10 (13860) Misc. bond : bond 0.13866 / 9.47 ( 258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 0.335 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: E 3 TYR cc_start: 0.7192 (m-80) cc_final: 0.6628 (m-80) REVERT: A 3 TYR cc_start: 0.7448 (m-80) cc_final: 0.6967 (t80) REVERT: F 3 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: I 3 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: L 3 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: N 3 TYR cc_start: 0.6186 (m-80) cc_final: 0.5759 (t80) REVERT: P 3 TYR cc_start: 0.7258 (m-80) cc_final: 0.6654 (m-10) REVERT: R 7 ILE cc_start: 0.8500 (mt) cc_final: 0.8284 (mp) REVERT: T 3 TYR cc_start: 0.7461 (m-80) cc_final: 0.7194 (t80) REVERT: V 3 TYR cc_start: 0.8285 (m-80) cc_final: 0.7160 (t80) REVERT: X 3 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: 1 3 TYR cc_start: 0.7304 (m-80) cc_final: 0.5832 (p90) REVERT: 3 3 TYR cc_start: 0.8038 (m-80) cc_final: 0.7278 (p90) REVERT: 4 3 TYR cc_start: 0.6381 (m-80) cc_final: 0.6114 (t80) REVERT: 4 11 LYS cc_start: 0.7601 (tptt) cc_final: 0.6090 (tttt) REVERT: 7 7 ILE cc_start: 0.8761 (mt) cc_final: 0.8558 (mp) REVERT: 8 11 LYS cc_start: 0.7149 (mmtt) cc_final: 0.5608 (tmmm) REVERT: b 3 TYR cc_start: 0.7304 (m-80) cc_final: 0.7016 (t80) REVERT: d 3 TYR cc_start: 0.7546 (m-80) cc_final: 0.6622 (m-80) REVERT: f 3 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: j 3 TYR cc_start: 0.7081 (m-80) cc_final: 0.6807 (m-80) REVERT: k 3 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: m 3 TYR cc_start: 0.6312 (m-80) cc_final: 0.5898 (m-80) REVERT: n 3 TYR cc_start: 0.7369 (m-80) cc_final: 0.7076 (m-10) REVERT: t 3 TYR cc_start: 0.7394 (m-80) cc_final: 0.7003 (t80) REVERT: AD 3 TYR cc_start: 0.7548 (m-80) cc_final: 0.6566 (m-80) REVERT: AE 3 TYR cc_start: 0.6004 (m-80) cc_final: 0.5665 (m-80) REVERT: AL 3 TYR cc_start: 0.7419 (m-80) cc_final: 0.6763 (t80) REVERT: AN 3 TYR cc_start: 0.7688 (m-80) cc_final: 0.6769 (t80) REVERT: AQ 3 TYR cc_start: 0.7014 (m-80) cc_final: 0.6675 (m-80) REVERT: AS 3 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6904 (m-80) REVERT: AV 3 TYR cc_start: 0.7366 (m-80) cc_final: 0.6445 (m-80) REVERT: AW 3 TYR cc_start: 0.6192 (m-80) cc_final: 0.5519 (t80) REVERT: AX 3 TYR cc_start: 0.7275 (m-80) cc_final: 0.6766 (m-10) REVERT: AZ 7 ILE cc_start: 0.8395 (mt) cc_final: 0.8192 (mp) REVERT: A3 3 TYR cc_start: 0.7417 (m-80) cc_final: 0.7025 (t80) REVERT: A5 3 TYR cc_start: 0.7883 (m-80) cc_final: 0.6199 (t80) REVERT: BA 3 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6759 (m-10) REVERT: BD 3 TYR cc_start: 0.7452 (m-80) cc_final: 0.6937 (m-80) REVERT: BE 3 TYR cc_start: 0.6432 (m-80) cc_final: 0.5447 (t80) REVERT: BI 11 LYS cc_start: 0.7641 (mmtt) cc_final: 0.6518 (mmmt) REVERT: BK 7 ILE cc_start: 0.8248 (mt) cc_final: 0.8047 (mp) REVERT: BN 3 TYR cc_start: 0.7250 (m-80) cc_final: 0.6682 (m-80) REVERT: BQ 3 TYR cc_start: 0.7010 (m-80) cc_final: 0.6787 (m-80) REVERT: BS 3 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: BT 3 TYR cc_start: 0.6943 (m-80) cc_final: 0.6287 (m-80) REVERT: BV 3 TYR cc_start: 0.7208 (m-80) cc_final: 0.6620 (m-80) REVERT: BW 3 TYR cc_start: 0.6024 (m-80) cc_final: 0.5161 (t80) outliers start: 28 outliers final: 4 residues processed: 251 average time/residue: 0.1707 time to fit residues: 52.7401 Evaluate side-chains 177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 TYR Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain L residue 3 TYR Chi-restraints excluded: chain X residue 3 TYR Chi-restraints excluded: chain f residue 3 TYR Chi-restraints excluded: chain i residue 3 TYR Chi-restraints excluded: chain k residue 3 TYR Chi-restraints excluded: chain x residue 3 TYR Chi-restraints excluded: chain AP residue 3 TYR Chi-restraints excluded: chain AS residue 3 TYR Chi-restraints excluded: chain A7 residue 3 TYR Chi-restraints excluded: chain BA residue 3 TYR Chi-restraints excluded: chain BS residue 3 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 2 HIS R 2 HIS b 2 HIS h 2 HIS p 2 HIS t 2 HIS y 2 HIS AE 2 HIS AH 2 HIS AL 2 HIS AQ 2 HIS AW 2 HIS AZ 2 HIS A3 2 HIS A8 2 HIS A9 2 HIS BE 2 HIS BH 2 HIS BQ 2 HIS BR 2 HIS BW 2 HIS BZ 2 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.178671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.128229 restraints weight = 11210.483| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.67 r_work: 0.4004 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10968 Z= 0.149 Angle : 0.591 4.555 13860 Z= 0.267 Chirality : 0.062 0.151 1386 Planarity : 0.004 0.028 1512 Dihedral : 8.609 61.696 2042 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.88 % Allowed : 12.20 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.24), residues: 1008 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.003 TYRAD 3 HIS 0.004 0.001 HISA8 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (10710) covalent geometry : angle 0.59096 / 0.27 (13860) Misc. bond : bond 0.00062 / 0.04 ( 258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 TYR cc_start: 0.7287 (m-80) cc_final: 0.6180 (t80) REVERT: M 3 TYR cc_start: 0.7318 (m-80) cc_final: 0.6715 (m-80) REVERT: N 3 TYR cc_start: 0.6071 (m-80) cc_final: 0.5864 (t80) REVERT: P 3 TYR cc_start: 0.6790 (m-80) cc_final: 0.6176 (m-10) REVERT: V 3 TYR cc_start: 0.7125 (m-80) cc_final: 0.6576 (t80) REVERT: Y 3 TYR cc_start: 0.7053 (m-80) cc_final: 0.6417 (m-80) REVERT: 0 3 TYR cc_start: 0.6942 (m-80) cc_final: 0.6740 (m-80) REVERT: 8 11 LYS cc_start: 0.7631 (mmtt) cc_final: 0.5872 (tmtp) REVERT: a 3 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.5913 (t80) REVERT: d 3 TYR cc_start: 0.6907 (m-80) cc_final: 0.6516 (m-80) REVERT: m 3 TYR cc_start: 0.5958 (m-80) cc_final: 0.5656 (m-80) REVERT: v 3 TYR cc_start: 0.7158 (m-80) cc_final: 0.5573 (t80) REVERT: AA 3 TYR cc_start: 0.6863 (m-80) cc_final: 0.6635 (m-80) REVERT: AB 3 TYR cc_start: 0.6400 (m-80) cc_final: 0.6198 (m-80) REVERT: AD 3 TYR cc_start: 0.7419 (m-80) cc_final: 0.6485 (t80) REVERT: AF 3 TYR cc_start: 0.6771 (m-80) cc_final: 0.6216 (m-80) REVERT: AL 3 TYR cc_start: 0.7033 (m-80) cc_final: 0.6745 (t80) REVERT: AM 10 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8292 (p) REVERT: AN 3 TYR cc_start: 0.6881 (m-80) cc_final: 0.5924 (t80) REVERT: AQ 3 TYR cc_start: 0.6554 (m-80) cc_final: 0.6124 (m-80) REVERT: AV 3 TYR cc_start: 0.7234 (m-80) cc_final: 0.6124 (t80) REVERT: AW 3 TYR cc_start: 0.5835 (m-80) cc_final: 0.5551 (m-80) REVERT: AX 3 TYR cc_start: 0.6872 (m-80) cc_final: 0.6362 (m-10) REVERT: A5 3 TYR cc_start: 0.7020 (m-80) cc_final: 0.6251 (t80) REVERT: A8 3 TYR cc_start: 0.6602 (m-80) cc_final: 0.5897 (m-80) REVERT: BA 3 TYR cc_start: 0.6671 (m-80) cc_final: 0.6068 (m-10) REVERT: BD 3 TYR cc_start: 0.7207 (m-80) cc_final: 0.6035 (t80) REVERT: BE 3 TYR cc_start: 0.6019 (m-80) cc_final: 0.5711 (t80) REVERT: BE 11 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8052 (mptt) REVERT: BF 3 TYR cc_start: 0.6983 (m-80) cc_final: 0.6468 (m-10) REVERT: BI 11 LYS cc_start: 0.7696 (mmtt) cc_final: 0.6653 (mmmt) REVERT: BQ 3 TYR cc_start: 0.6860 (m-80) cc_final: 0.6408 (m-80) REVERT: BS 3 TYR cc_start: 0.7407 (m-80) cc_final: 0.6522 (m-80) REVERT: BT 3 TYR cc_start: 0.6795 (m-80) cc_final: 0.6330 (t80) REVERT: BV 3 TYR cc_start: 0.7164 (m-80) cc_final: 0.6738 (m-80) REVERT: BW 3 TYR cc_start: 0.5547 (m-80) cc_final: 0.5023 (t80) outliers start: 29 outliers final: 20 residues processed: 147 average time/residue: 0.1791 time to fit residues: 32.1755 Evaluate side-chains 146 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain a residue 3 TYR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain AD residue 10 SER Chi-restraints excluded: chain AH residue 10 SER Chi-restraints excluded: chain AK residue 10 SER Chi-restraints excluded: chain AM residue 10 SER Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AQ residue 10 SER Chi-restraints excluded: chain AV residue 10 SER Chi-restraints excluded: chain AW residue 10 SER Chi-restraints excluded: chain A2 residue 10 SER Chi-restraints excluded: chain BD residue 10 SER Chi-restraints excluded: chain BE residue 11 LYS Chi-restraints excluded: chain BV residue 10 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 86 optimal weight: 0.0570 chunk 53 optimal weight: 9.9990 chunk 121 optimal weight: 0.0470 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 2 HIS g 2 HIS A9 2 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.175431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.123422 restraints weight = 11847.952| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 3.82 r_work: 0.3950 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10968 Z= 0.215 Angle : 0.613 4.468 13860 Z= 0.277 Chirality : 0.062 0.141 1386 Planarity : 0.004 0.031 1512 Dihedral : 10.051 51.953 2016 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.17 % Allowed : 12.80 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.24), residues: 1008 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.002 TYRAB 3 HIS 0.007 0.001 HISAE 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (10710) covalent geometry : angle 0.61325 / 0.28 (13860) Misc. bond : bond 0.00111 / 0.08 ( 258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.442 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: C 3 TYR cc_start: 0.7466 (m-80) cc_final: 0.6358 (t80) REVERT: M 3 TYR cc_start: 0.7210 (m-80) cc_final: 0.6628 (m-80) REVERT: N 3 TYR cc_start: 0.6180 (m-80) cc_final: 0.5785 (t80) REVERT: P 3 TYR cc_start: 0.6916 (m-80) cc_final: 0.6338 (m-10) REVERT: V 3 TYR cc_start: 0.7209 (m-80) cc_final: 0.6580 (t80) REVERT: Y 3 TYR cc_start: 0.7019 (m-80) cc_final: 0.6278 (m-80) REVERT: 0 3 TYR cc_start: 0.7024 (m-80) cc_final: 0.6795 (m-80) REVERT: 3 3 TYR cc_start: 0.7163 (m-80) cc_final: 0.6275 (p90) REVERT: 4 3 TYR cc_start: 0.7084 (m-80) cc_final: 0.6226 (t80) REVERT: 4 11 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.6747 (tttt) REVERT: 8 11 LYS cc_start: 0.7879 (mmtt) cc_final: 0.6196 (tmmm) REVERT: a 3 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.5982 (t80) REVERT: c 10 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8438 (p) REVERT: d 3 TYR cc_start: 0.6972 (m-80) cc_final: 0.6528 (m-80) REVERT: e 2 HIS cc_start: 0.5516 (m-70) cc_final: 0.5241 (t70) REVERT: l 3 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6225 (m-80) REVERT: v 3 TYR cc_start: 0.7300 (m-80) cc_final: 0.5638 (t80) REVERT: AF 3 TYR cc_start: 0.6709 (m-80) cc_final: 0.6192 (m-80) REVERT: AL 3 TYR cc_start: 0.7184 (m-80) cc_final: 0.6811 (t80) REVERT: AN 3 TYR cc_start: 0.6712 (m-80) cc_final: 0.5686 (t80) REVERT: AQ 3 TYR cc_start: 0.6616 (m-80) cc_final: 0.6209 (m-80) REVERT: AT 3 TYR cc_start: 0.6359 (m-80) cc_final: 0.6041 (t80) REVERT: AV 3 TYR cc_start: 0.7177 (m-80) cc_final: 0.6532 (t80) REVERT: AW 3 TYR cc_start: 0.5881 (m-80) cc_final: 0.5515 (m-80) REVERT: A4 10 SER cc_start: 0.8092 (OUTLIER) cc_final: 0.7884 (p) REVERT: A5 3 TYR cc_start: 0.6976 (m-80) cc_final: 0.6680 (m-80) REVERT: A6 3 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: A8 3 TYR cc_start: 0.6740 (m-80) cc_final: 0.6031 (m-80) REVERT: BD 3 TYR cc_start: 0.7264 (m-80) cc_final: 0.6949 (m-80) REVERT: BE 3 TYR cc_start: 0.6336 (m-80) cc_final: 0.5802 (t80) REVERT: BK 7 ILE cc_start: 0.8259 (mt) cc_final: 0.8043 (mp) REVERT: BO 3 TYR cc_start: 0.7498 (m-80) cc_final: 0.7297 (m-80) REVERT: BQ 3 TYR cc_start: 0.6907 (m-80) cc_final: 0.6430 (m-80) REVERT: BR 3 TYR cc_start: 0.6994 (m-80) cc_final: 0.6710 (m-80) REVERT: BT 3 TYR cc_start: 0.6725 (m-80) cc_final: 0.6216 (t80) REVERT: BW 3 TYR cc_start: 0.5932 (m-80) cc_final: 0.5389 (t80) outliers start: 32 outliers final: 17 residues processed: 146 average time/residue: 0.2039 time to fit residues: 35.6087 Evaluate side-chains 146 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 11 LYS Chi-restraints excluded: chain a residue 3 TYR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain AK residue 10 SER Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AV residue 10 SER Chi-restraints excluded: chain AW residue 10 SER Chi-restraints excluded: chain A4 residue 10 SER Chi-restraints excluded: chain A6 residue 3 TYR Chi-restraints excluded: chain A8 residue 10 SER Chi-restraints excluded: chain BE residue 11 LYS Chi-restraints excluded: chain BV residue 10 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 0.3980 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.173532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.119824 restraints weight = 13378.232| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 4.07 r_work: 0.3900 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 10968 Z= 0.375 Angle : 0.770 5.695 13860 Z= 0.354 Chirality : 0.067 0.141 1386 Planarity : 0.005 0.037 1512 Dihedral : 15.346 73.483 2016 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.86 % Allowed : 12.70 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.25), residues: 1008 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.003 TYRAS 3 HIS 0.009 0.001 HIS B 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00896 / 0.38 (10710) covalent geometry : angle 0.76975 / 0.35 (13860) Misc. bond : bond 0.00166 / 0.11 ( 258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 0.433 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: K 3 TYR cc_start: 0.6547 (m-80) cc_final: 0.6171 (t80) REVERT: M 3 TYR cc_start: 0.7361 (m-80) cc_final: 0.6801 (m-80) REVERT: N 3 TYR cc_start: 0.6723 (m-80) cc_final: 0.6338 (t80) REVERT: P 3 TYR cc_start: 0.7115 (m-80) cc_final: 0.6511 (m-10) REVERT: X 2 HIS cc_start: 0.4840 (OUTLIER) cc_final: 0.4337 (m170) REVERT: Y 3 TYR cc_start: 0.7111 (m-80) cc_final: 0.6276 (m-80) REVERT: 0 3 TYR cc_start: 0.6950 (m-80) cc_final: 0.6720 (m-80) REVERT: 1 3 TYR cc_start: 0.6809 (m-80) cc_final: 0.5401 (p90) REVERT: 3 3 TYR cc_start: 0.7519 (m-80) cc_final: 0.6501 (p90) REVERT: 4 3 TYR cc_start: 0.7133 (m-80) cc_final: 0.6285 (t80) REVERT: 4 11 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.6950 (tttt) REVERT: 8 11 LYS cc_start: 0.8136 (mmtt) cc_final: 0.6308 (tttm) REVERT: a 3 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6397 (t80) REVERT: e 2 HIS cc_start: 0.5784 (m-70) cc_final: 0.5343 (t70) REVERT: f 2 HIS cc_start: 0.5115 (m-70) cc_final: 0.4890 (m90) REVERT: k 3 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.5902 (m-80) REVERT: l 3 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.6441 (m-80) REVERT: m 3 TYR cc_start: 0.6646 (m-80) cc_final: 0.6268 (m-80) REVERT: w 3 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: AF 3 TYR cc_start: 0.6886 (m-80) cc_final: 0.6590 (m-10) REVERT: AN 3 TYR cc_start: 0.7207 (m-80) cc_final: 0.6403 (t80) REVERT: AQ 3 TYR cc_start: 0.6745 (m-80) cc_final: 0.6494 (m-80) REVERT: AT 3 TYR cc_start: 0.6658 (m-80) cc_final: 0.6161 (t80) REVERT: AV 3 TYR cc_start: 0.7260 (m-80) cc_final: 0.6552 (t80) REVERT: AW 3 TYR cc_start: 0.6434 (m-80) cc_final: 0.6134 (m-80) REVERT: AX 3 TYR cc_start: 0.7041 (m-80) cc_final: 0.6543 (m-10) REVERT: A5 3 TYR cc_start: 0.7401 (m-80) cc_final: 0.7050 (m-80) REVERT: A6 3 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: A8 3 TYR cc_start: 0.7140 (m-80) cc_final: 0.6478 (m-80) REVERT: BD 3 TYR cc_start: 0.7376 (m-80) cc_final: 0.6671 (m-80) REVERT: BE 3 TYR cc_start: 0.6435 (m-80) cc_final: 0.5924 (t80) REVERT: BE 11 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8262 (mptt) REVERT: BJ 3 TYR cc_start: 0.5943 (m-80) cc_final: 0.5681 (m-80) REVERT: BQ 3 TYR cc_start: 0.7124 (m-80) cc_final: 0.6536 (m-80) REVERT: BT 3 TYR cc_start: 0.6861 (m-80) cc_final: 0.6259 (t80) REVERT: BW 3 TYR cc_start: 0.6174 (m-80) cc_final: 0.5491 (m-80) outliers start: 49 outliers final: 23 residues processed: 162 average time/residue: 0.2432 time to fit residues: 46.7809 Evaluate side-chains 157 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 11 LYS Chi-restraints excluded: chain a residue 3 TYR Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain k residue 3 TYR Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain w residue 3 TYR Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain AE residue 11 LYS Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AV residue 10 SER Chi-restraints excluded: chain AW residue 10 SER Chi-restraints excluded: chain AW residue 11 LYS Chi-restraints excluded: chain A6 residue 3 TYR Chi-restraints excluded: chain A8 residue 10 SER Chi-restraints excluded: chain BE residue 11 LYS Chi-restraints excluded: chain BV residue 10 SER Chi-restraints excluded: chain BW residue 11 LYS Chi-restraints excluded: chain B0 residue 10 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 46 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 2 HIS y 2 HIS AQ 2 HIS A8 2 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.176370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.122099 restraints weight = 13692.791| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 4.11 r_work: 0.3957 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10968 Z= 0.166 Angle : 0.574 4.468 13860 Z= 0.256 Chirality : 0.062 0.135 1386 Planarity : 0.004 0.034 1512 Dihedral : 12.323 74.020 2016 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.67 % Allowed : 13.89 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.25), residues: 1008 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.002 TYRAU 3 HIS 0.007 0.001 HISAQ 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (10710) covalent geometry : angle 0.57378 / 0.26 (13860) Misc. bond : bond 0.00072 / 0.05 ( 258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.424 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: C 3 TYR cc_start: 0.7480 (m-80) cc_final: 0.6368 (t80) REVERT: I 3 TYR cc_start: 0.6565 (m-80) cc_final: 0.6355 (m-80) REVERT: K 3 TYR cc_start: 0.6472 (m-80) cc_final: 0.6149 (t80) REVERT: M 3 TYR cc_start: 0.7208 (m-80) cc_final: 0.6554 (m-80) REVERT: N 3 TYR cc_start: 0.6573 (m-80) cc_final: 0.6222 (t80) REVERT: P 3 TYR cc_start: 0.6996 (m-80) cc_final: 0.6385 (m-10) REVERT: V 3 TYR cc_start: 0.7400 (m-80) cc_final: 0.6398 (t80) REVERT: Y 3 TYR cc_start: 0.6947 (m-80) cc_final: 0.6197 (m-80) REVERT: 0 3 TYR cc_start: 0.6968 (m-80) cc_final: 0.6759 (m-80) REVERT: 3 3 TYR cc_start: 0.7367 (m-80) cc_final: 0.6256 (p90) REVERT: 4 3 TYR cc_start: 0.7051 (m-80) cc_final: 0.6249 (t80) REVERT: 4 11 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.6791 (tttt) REVERT: 8 11 LYS cc_start: 0.8122 (mmtt) cc_final: 0.6217 (tttm) REVERT: a 3 TYR cc_start: 0.7063 (OUTLIER) cc_final: 0.6043 (t80) REVERT: e 2 HIS cc_start: 0.5806 (m-70) cc_final: 0.5515 (t70) REVERT: l 3 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6385 (m-80) REVERT: m 3 TYR cc_start: 0.6428 (m-80) cc_final: 0.6044 (m-80) REVERT: v 3 TYR cc_start: 0.7571 (m-80) cc_final: 0.6145 (t80) REVERT: w 3 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.7061 (m-10) REVERT: AA 3 TYR cc_start: 0.7002 (m-80) cc_final: 0.6595 (m-80) REVERT: AF 3 TYR cc_start: 0.6780 (m-80) cc_final: 0.6488 (m-10) REVERT: AL 3 TYR cc_start: 0.7433 (m-80) cc_final: 0.6907 (t80) REVERT: AN 3 TYR cc_start: 0.7269 (m-80) cc_final: 0.6018 (t80) REVERT: AS 3 TYR cc_start: 0.6888 (m-80) cc_final: 0.6643 (m-80) REVERT: AT 3 TYR cc_start: 0.6652 (m-80) cc_final: 0.6150 (t80) REVERT: AV 3 TYR cc_start: 0.7198 (m-80) cc_final: 0.6536 (t80) REVERT: AW 3 TYR cc_start: 0.6225 (m-80) cc_final: 0.5907 (m-80) REVERT: AX 3 TYR cc_start: 0.6954 (m-80) cc_final: 0.6499 (m-10) REVERT: A5 3 TYR cc_start: 0.7355 (m-80) cc_final: 0.6960 (m-80) REVERT: A6 3 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7421 (m-10) REVERT: A8 3 TYR cc_start: 0.7013 (m-80) cc_final: 0.6344 (m-80) REVERT: BD 3 TYR cc_start: 0.7205 (m-80) cc_final: 0.6953 (m-80) REVERT: BE 3 TYR cc_start: 0.6261 (m-80) cc_final: 0.5741 (t80) REVERT: BQ 3 TYR cc_start: 0.6992 (m-80) cc_final: 0.6343 (m-80) REVERT: BT 3 TYR cc_start: 0.6831 (m-80) cc_final: 0.6358 (t80) REVERT: BW 3 TYR cc_start: 0.6084 (m-80) cc_final: 0.5466 (m-80) outliers start: 37 outliers final: 23 residues processed: 148 average time/residue: 0.2312 time to fit residues: 40.3769 Evaluate side-chains 147 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 11 LYS Chi-restraints excluded: chain a residue 3 TYR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain t residue 10 SER Chi-restraints excluded: chain w residue 3 TYR Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain AE residue 11 LYS Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AV residue 10 SER Chi-restraints excluded: chain AW residue 10 SER Chi-restraints excluded: chain AW residue 11 LYS Chi-restraints excluded: chain A0 residue 10 SER Chi-restraints excluded: chain A6 residue 3 TYR Chi-restraints excluded: chain A8 residue 10 SER Chi-restraints excluded: chain BE residue 11 LYS Chi-restraints excluded: chain BV residue 10 SER Chi-restraints excluded: chain BW residue 11 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 HIS BW 2 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.175918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.121563 restraints weight = 13593.469| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 4.10 r_work: 0.3941 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10968 Z= 0.245 Angle : 0.634 4.270 13860 Z= 0.286 Chirality : 0.063 0.139 1386 Planarity : 0.004 0.033 1512 Dihedral : 13.362 83.258 2016 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.57 % Allowed : 14.19 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.25), residues: 1008 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.002 TYR k 3 HIS 0.005 0.001 HIS x 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 (10710) covalent geometry : angle 0.63396 / 0.29 (13860) Misc. bond : bond 0.00105 / 0.07 ( 258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.406 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: C 3 TYR cc_start: 0.7539 (m-80) cc_final: 0.6027 (t80) REVERT: K 3 TYR cc_start: 0.6541 (m-80) cc_final: 0.6162 (t80) REVERT: M 3 TYR cc_start: 0.7251 (m-80) cc_final: 0.6558 (m-80) REVERT: N 3 TYR cc_start: 0.6603 (m-80) cc_final: 0.6142 (t80) REVERT: P 3 TYR cc_start: 0.7151 (m-80) cc_final: 0.6577 (m-10) REVERT: V 3 TYR cc_start: 0.7450 (m-80) cc_final: 0.6386 (t80) REVERT: X 2 HIS cc_start: 0.4882 (OUTLIER) cc_final: 0.4345 (m170) REVERT: Y 3 TYR cc_start: 0.7023 (m-80) cc_final: 0.6092 (m-80) REVERT: 0 3 TYR cc_start: 0.6907 (m-80) cc_final: 0.6690 (m-80) REVERT: 1 3 TYR cc_start: 0.6807 (m-80) cc_final: 0.5425 (p90) REVERT: 3 3 TYR cc_start: 0.7505 (m-80) cc_final: 0.6279 (p90) REVERT: 4 3 TYR cc_start: 0.7090 (m-80) cc_final: 0.6291 (t80) REVERT: 4 11 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.6848 (tttt) REVERT: 8 11 LYS cc_start: 0.8053 (mmtt) cc_final: 0.6189 (tttm) REVERT: a 3 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6263 (t80) REVERT: d 3 TYR cc_start: 0.7433 (m-80) cc_final: 0.6150 (t80) REVERT: e 3 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6834 (m-10) REVERT: g 3 TYR cc_start: 0.6839 (m-80) cc_final: 0.6637 (m-80) REVERT: l 3 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6376 (m-80) REVERT: m 3 TYR cc_start: 0.6608 (m-80) cc_final: 0.6282 (m-80) REVERT: v 3 TYR cc_start: 0.7599 (m-80) cc_final: 0.6016 (t80) REVERT: w 3 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.7024 (m-10) REVERT: y 3 TYR cc_start: 0.6919 (m-80) cc_final: 0.6269 (m-80) REVERT: AA 3 TYR cc_start: 0.7090 (m-80) cc_final: 0.6749 (m-80) REVERT: AF 3 TYR cc_start: 0.6864 (m-80) cc_final: 0.6598 (m-10) REVERT: AL 3 TYR cc_start: 0.7503 (m-80) cc_final: 0.7024 (t80) REVERT: AN 3 TYR cc_start: 0.7299 (m-80) cc_final: 0.6041 (t80) REVERT: AQ 3 TYR cc_start: 0.7023 (m-80) cc_final: 0.6166 (m-80) REVERT: AS 3 TYR cc_start: 0.6859 (m-80) cc_final: 0.6562 (m-80) REVERT: AT 3 TYR cc_start: 0.6762 (m-80) cc_final: 0.6216 (t80) REVERT: AV 3 TYR cc_start: 0.7199 (m-80) cc_final: 0.6551 (t80) REVERT: AW 3 TYR cc_start: 0.6391 (m-80) cc_final: 0.6074 (m-80) REVERT: AW 11 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8058 (mptt) REVERT: AX 3 TYR cc_start: 0.6974 (m-80) cc_final: 0.6506 (m-10) REVERT: A5 3 TYR cc_start: 0.7461 (m-80) cc_final: 0.7088 (m-80) REVERT: A6 3 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7463 (m-10) REVERT: A8 3 TYR cc_start: 0.7196 (m-80) cc_final: 0.6280 (m-80) REVERT: BB 3 TYR cc_start: 0.6408 (m-80) cc_final: 0.5952 (m-80) REVERT: BD 3 TYR cc_start: 0.7254 (m-80) cc_final: 0.6309 (m-80) REVERT: BE 3 TYR cc_start: 0.6318 (m-80) cc_final: 0.5811 (t80) REVERT: BE 11 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8341 (mptt) REVERT: BJ 3 TYR cc_start: 0.5812 (m-80) cc_final: 0.5523 (m-80) REVERT: BQ 3 TYR cc_start: 0.7084 (m-80) cc_final: 0.6383 (m-80) REVERT: BT 3 TYR cc_start: 0.6917 (m-80) cc_final: 0.6356 (t80) REVERT: BW 3 TYR cc_start: 0.6179 (m-80) cc_final: 0.5448 (m-80) outliers start: 36 outliers final: 26 residues processed: 154 average time/residue: 0.2303 time to fit residues: 41.9311 Evaluate side-chains 158 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 11 LYS Chi-restraints excluded: chain a residue 3 TYR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain e residue 3 TYR Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain t residue 10 SER Chi-restraints excluded: chain w residue 3 TYR Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain z residue 10 SER Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AE residue 11 LYS Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AV residue 10 SER Chi-restraints excluded: chain AW residue 10 SER Chi-restraints excluded: chain AW residue 11 LYS Chi-restraints excluded: chain A0 residue 10 SER Chi-restraints excluded: chain A6 residue 3 TYR Chi-restraints excluded: chain A8 residue 10 SER Chi-restraints excluded: chain BE residue 11 LYS Chi-restraints excluded: chain BV residue 10 SER Chi-restraints excluded: chain BW residue 11 LYS Chi-restraints excluded: chain B0 residue 10 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 2 HIS ** e 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.177755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.122844 restraints weight = 13816.369| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 4.16 r_work: 0.3968 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10968 Z= 0.166 Angle : 0.559 4.024 13860 Z= 0.249 Chirality : 0.062 0.136 1386 Planarity : 0.004 0.034 1512 Dihedral : 11.862 85.333 2016 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.27 % Allowed : 15.18 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.25), residues: 1008 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.002 TYR i 3 HIS 0.004 0.001 HISBS 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (10710) covalent geometry : angle 0.55949 / 0.25 (13860) Misc. bond : bond 0.00071 / 0.05 ( 258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.347 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: C 3 TYR cc_start: 0.7488 (m-80) cc_final: 0.6074 (t80) REVERT: K 3 TYR cc_start: 0.6520 (m-80) cc_final: 0.6201 (t80) REVERT: M 3 TYR cc_start: 0.7309 (m-80) cc_final: 0.6528 (m-80) REVERT: N 3 TYR cc_start: 0.6514 (m-80) cc_final: 0.6120 (t80) REVERT: P 3 TYR cc_start: 0.7124 (m-80) cc_final: 0.6558 (m-10) REVERT: V 3 TYR cc_start: 0.7284 (m-80) cc_final: 0.6348 (t80) REVERT: X 2 HIS cc_start: 0.4959 (OUTLIER) cc_final: 0.4412 (m170) REVERT: Y 3 TYR cc_start: 0.7048 (m-80) cc_final: 0.5956 (p90) REVERT: 0 3 TYR cc_start: 0.6855 (m-80) cc_final: 0.6640 (m-80) REVERT: 3 3 TYR cc_start: 0.7257 (m-80) cc_final: 0.5956 (p90) REVERT: 4 3 TYR cc_start: 0.6915 (m-80) cc_final: 0.6138 (t80) REVERT: 4 11 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.6808 (tttt) REVERT: 6 3 TYR cc_start: 0.6923 (m-80) cc_final: 0.5857 (t80) REVERT: 8 11 LYS cc_start: 0.8031 (mmtt) cc_final: 0.6126 (tttm) REVERT: a 3 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.6060 (t80) REVERT: d 3 TYR cc_start: 0.7397 (m-80) cc_final: 0.6099 (t80) REVERT: l 3 TYR cc_start: 0.7348 (m-80) cc_final: 0.6383 (m-80) REVERT: v 3 TYR cc_start: 0.7633 (m-80) cc_final: 0.6147 (t80) REVERT: w 3 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.7051 (m-10) REVERT: y 3 TYR cc_start: 0.6819 (m-80) cc_final: 0.6187 (m-80) REVERT: AF 3 TYR cc_start: 0.6830 (m-80) cc_final: 0.6541 (m-10) REVERT: AL 3 TYR cc_start: 0.7450 (m-80) cc_final: 0.6946 (t80) REVERT: AN 3 TYR cc_start: 0.7303 (m-80) cc_final: 0.6063 (t80) REVERT: AQ 3 TYR cc_start: 0.6912 (m-80) cc_final: 0.6217 (m-80) REVERT: AT 3 TYR cc_start: 0.6750 (m-80) cc_final: 0.6173 (t80) REVERT: AV 3 TYR cc_start: 0.7158 (m-80) cc_final: 0.6510 (t80) REVERT: AW 3 TYR cc_start: 0.6253 (m-80) cc_final: 0.5926 (m-80) REVERT: AW 11 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7965 (mptt) REVERT: AX 3 TYR cc_start: 0.6860 (m-80) cc_final: 0.6419 (m-10) REVERT: A5 3 TYR cc_start: 0.7452 (m-80) cc_final: 0.7118 (m-80) REVERT: A8 3 TYR cc_start: 0.7095 (m-80) cc_final: 0.6230 (m-80) REVERT: BB 3 TYR cc_start: 0.6468 (m-80) cc_final: 0.6010 (m-80) REVERT: BD 3 TYR cc_start: 0.7258 (m-80) cc_final: 0.6897 (m-80) REVERT: BE 3 TYR cc_start: 0.6054 (m-80) cc_final: 0.5396 (t80) REVERT: BJ 3 TYR cc_start: 0.5651 (m-80) cc_final: 0.5342 (m-80) REVERT: BQ 3 TYR cc_start: 0.7026 (m-80) cc_final: 0.6343 (m-80) REVERT: BT 3 TYR cc_start: 0.6784 (m-80) cc_final: 0.6257 (t80) REVERT: BW 3 TYR cc_start: 0.6161 (m-80) cc_final: 0.5490 (t80) outliers start: 33 outliers final: 26 residues processed: 146 average time/residue: 0.2285 time to fit residues: 39.3353 Evaluate side-chains 148 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 11 LYS Chi-restraints excluded: chain a residue 3 TYR Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain t residue 10 SER Chi-restraints excluded: chain w residue 3 TYR Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AE residue 11 LYS Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AW residue 10 SER Chi-restraints excluded: chain AW residue 11 LYS Chi-restraints excluded: chain A0 residue 10 SER Chi-restraints excluded: chain A2 residue 10 SER Chi-restraints excluded: chain A8 residue 10 SER Chi-restraints excluded: chain BE residue 11 LYS Chi-restraints excluded: chain BV residue 10 SER Chi-restraints excluded: chain BW residue 11 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 53 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 25 optimal weight: 0.0030 chunk 105 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 2 HIS ** e 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.180371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.125383 restraints weight = 13602.160| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 4.15 r_work: 0.4002 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10968 Z= 0.110 Angle : 0.510 4.195 13860 Z= 0.226 Chirality : 0.061 0.134 1386 Planarity : 0.004 0.034 1512 Dihedral : 9.624 63.499 2016 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.68 % Allowed : 15.87 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.25), residues: 1008 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.002 TYRAS 3 HIS 0.005 0.000 HISBS 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (10710) covalent geometry : angle 0.50956 / 0.23 (13860) Misc. bond : bond 0.00042 / 0.03 ( 258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.486 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: C 3 TYR cc_start: 0.7495 (m-80) cc_final: 0.6088 (t80) REVERT: M 3 TYR cc_start: 0.7280 (m-80) cc_final: 0.6428 (m-80) REVERT: P 3 TYR cc_start: 0.7034 (m-80) cc_final: 0.6483 (m-10) REVERT: V 3 TYR cc_start: 0.7256 (m-80) cc_final: 0.6297 (t80) REVERT: X 2 HIS cc_start: 0.4950 (OUTLIER) cc_final: 0.4409 (m170) REVERT: Y 3 TYR cc_start: 0.7057 (m-80) cc_final: 0.5889 (p90) REVERT: 0 3 TYR cc_start: 0.6722 (m-80) cc_final: 0.6431 (m-80) REVERT: 3 3 TYR cc_start: 0.7146 (m-80) cc_final: 0.5866 (p90) REVERT: 4 3 TYR cc_start: 0.6903 (m-80) cc_final: 0.6056 (t80) REVERT: 4 11 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.6458 (tttp) REVERT: 8 11 LYS cc_start: 0.8003 (mmtt) cc_final: 0.5970 (tmmm) REVERT: a 3 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.5760 (t80) REVERT: d 3 TYR cc_start: 0.7352 (m-80) cc_final: 0.6165 (t80) REVERT: v 3 TYR cc_start: 0.7585 (m-80) cc_final: 0.6143 (t80) REVERT: w 3 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6927 (m-10) REVERT: y 3 TYR cc_start: 0.6899 (m-80) cc_final: 0.6226 (m-80) REVERT: AA 3 TYR cc_start: 0.7051 (m-80) cc_final: 0.6579 (m-80) REVERT: AE 3 TYR cc_start: 0.6491 (m-80) cc_final: 0.5859 (t80) REVERT: AF 3 TYR cc_start: 0.6797 (m-80) cc_final: 0.6491 (m-10) REVERT: AL 3 TYR cc_start: 0.7405 (m-80) cc_final: 0.6821 (t80) REVERT: AN 3 TYR cc_start: 0.7185 (m-80) cc_final: 0.5979 (t80) REVERT: AO 3 TYR cc_start: 0.7420 (m-80) cc_final: 0.7057 (m-80) REVERT: AQ 3 TYR cc_start: 0.6831 (m-80) cc_final: 0.6101 (m-80) REVERT: AS 3 TYR cc_start: 0.7049 (m-80) cc_final: 0.6712 (m-80) REVERT: AT 3 TYR cc_start: 0.6790 (m-80) cc_final: 0.6220 (t80) REVERT: AV 3 TYR cc_start: 0.7155 (m-80) cc_final: 0.6939 (m-80) REVERT: AW 11 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.7923 (mptt) REVERT: AX 3 TYR cc_start: 0.6829 (m-80) cc_final: 0.6399 (m-10) REVERT: A8 3 TYR cc_start: 0.7065 (m-80) cc_final: 0.6123 (m-80) REVERT: BB 3 TYR cc_start: 0.6505 (m-80) cc_final: 0.6032 (m-80) REVERT: BE 3 TYR cc_start: 0.5915 (m-80) cc_final: 0.5316 (t80) REVERT: BK 7 ILE cc_start: 0.8197 (mt) cc_final: 0.7988 (mp) REVERT: BQ 3 TYR cc_start: 0.6934 (m-80) cc_final: 0.6371 (m-80) REVERT: BT 3 TYR cc_start: 0.6833 (m-80) cc_final: 0.6309 (t80) REVERT: BW 3 TYR cc_start: 0.6075 (m-80) cc_final: 0.5444 (t80) outliers start: 27 outliers final: 20 residues processed: 140 average time/residue: 0.2273 time to fit residues: 37.6097 Evaluate side-chains 140 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 11 LYS Chi-restraints excluded: chain a residue 3 TYR Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain w residue 3 TYR Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AE residue 11 LYS Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AW residue 10 SER Chi-restraints excluded: chain AW residue 11 LYS Chi-restraints excluded: chain A2 residue 10 SER Chi-restraints excluded: chain A8 residue 10 SER Chi-restraints excluded: chain BV residue 10 SER Chi-restraints excluded: chain BW residue 11 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 102 optimal weight: 0.2980 chunk 57 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 2 HIS ** e 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.176479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.121749 restraints weight = 13504.215| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 4.10 r_work: 0.3944 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 10968 Z= 0.299 Angle : 0.669 4.499 13860 Z= 0.304 Chirality : 0.066 0.139 1386 Planarity : 0.004 0.031 1512 Dihedral : 13.048 65.548 2016 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 3.67 % Allowed : 15.18 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.25), residues: 1008 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.003 TYRAS 3 HIS 0.004 0.001 HIS X 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.30 (10710) covalent geometry : angle 0.66857 / 0.30 (13860) Misc. bond : bond 0.00128 / 0.09 ( 258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.388 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: C 3 TYR cc_start: 0.7575 (m-80) cc_final: 0.6134 (t80) REVERT: K 3 TYR cc_start: 0.6557 (m-80) cc_final: 0.6192 (t80) REVERT: L 3 TYR cc_start: 0.6573 (m-80) cc_final: 0.5758 (t80) REVERT: N 3 TYR cc_start: 0.6737 (m-80) cc_final: 0.6266 (t80) REVERT: P 3 TYR cc_start: 0.7271 (m-80) cc_final: 0.6711 (m-10) REVERT: V 3 TYR cc_start: 0.7430 (m-80) cc_final: 0.6464 (t80) REVERT: X 2 HIS cc_start: 0.4918 (OUTLIER) cc_final: 0.4375 (m170) REVERT: Y 3 TYR cc_start: 0.7106 (m-80) cc_final: 0.6173 (m-80) REVERT: 0 3 TYR cc_start: 0.6881 (m-80) cc_final: 0.6606 (m-80) REVERT: 1 3 TYR cc_start: 0.7199 (m-80) cc_final: 0.5623 (p90) REVERT: 2 3 TYR cc_start: 0.6628 (m-80) cc_final: 0.5757 (t80) REVERT: 3 2 HIS cc_start: 0.5746 (OUTLIER) cc_final: 0.5391 (t-90) REVERT: 3 3 TYR cc_start: 0.7346 (m-80) cc_final: 0.6057 (p90) REVERT: 4 3 TYR cc_start: 0.7086 (m-80) cc_final: 0.6317 (t80) REVERT: 4 11 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.6694 (tmtp) REVERT: 6 3 TYR cc_start: 0.7139 (m-80) cc_final: 0.6017 (t80) REVERT: 8 11 LYS cc_start: 0.8039 (mmtt) cc_final: 0.6133 (tmmm) REVERT: a 3 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6322 (t80) REVERT: d 3 TYR cc_start: 0.7479 (m-80) cc_final: 0.6187 (t80) REVERT: e 2 HIS cc_start: 0.5823 (t70) cc_final: 0.5532 (t-90) REVERT: e 3 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6823 (m-10) REVERT: g 3 TYR cc_start: 0.6856 (m-80) cc_final: 0.6596 (m-80) REVERT: m 3 TYR cc_start: 0.6728 (m-80) cc_final: 0.6503 (m-80) REVERT: v 3 TYR cc_start: 0.7583 (m-80) cc_final: 0.6117 (t80) REVERT: w 3 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.6989 (m-10) REVERT: y 3 TYR cc_start: 0.6986 (m-80) cc_final: 0.6240 (m-80) REVERT: AA 3 TYR cc_start: 0.7020 (m-80) cc_final: 0.6694 (m-80) REVERT: AF 3 TYR cc_start: 0.6960 (m-80) cc_final: 0.6663 (m-10) REVERT: AN 3 TYR cc_start: 0.7277 (m-80) cc_final: 0.6033 (t80) REVERT: AT 3 TYR cc_start: 0.6995 (m-80) cc_final: 0.6183 (t80) REVERT: AV 3 TYR cc_start: 0.7232 (m-80) cc_final: 0.6600 (t80) REVERT: AW 3 TYR cc_start: 0.6473 (m-80) cc_final: 0.6138 (m-80) REVERT: AW 11 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8034 (mptt) REVERT: AX 3 TYR cc_start: 0.6957 (m-80) cc_final: 0.6465 (m-10) REVERT: A8 3 TYR cc_start: 0.7197 (m-80) cc_final: 0.6609 (m-80) REVERT: BA 3 TYR cc_start: 0.6775 (m-10) cc_final: 0.6441 (m-10) REVERT: BB 3 TYR cc_start: 0.6538 (m-80) cc_final: 0.6035 (m-80) REVERT: BD 3 TYR cc_start: 0.7126 (m-80) cc_final: 0.6685 (m-80) REVERT: BE 3 TYR cc_start: 0.6144 (m-80) cc_final: 0.5513 (t80) REVERT: BJ 3 TYR cc_start: 0.5559 (m-80) cc_final: 0.5209 (m-80) REVERT: BQ 3 TYR cc_start: 0.7066 (m-80) cc_final: 0.6537 (m-80) REVERT: BT 3 TYR cc_start: 0.6966 (m-80) cc_final: 0.6399 (t80) REVERT: BW 3 TYR cc_start: 0.6274 (m-80) cc_final: 0.5604 (t80) outliers start: 37 outliers final: 28 residues processed: 155 average time/residue: 0.2347 time to fit residues: 43.3892 Evaluate side-chains 160 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain 3 residue 2 HIS Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 11 LYS Chi-restraints excluded: chain a residue 3 TYR Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain e residue 3 TYR Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain t residue 10 SER Chi-restraints excluded: chain w residue 3 TYR Chi-restraints excluded: chain y residue 10 SER Chi-restraints excluded: chain z residue 10 SER Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AE residue 11 LYS Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AV residue 10 SER Chi-restraints excluded: chain AW residue 10 SER Chi-restraints excluded: chain AW residue 11 LYS Chi-restraints excluded: chain A2 residue 10 SER Chi-restraints excluded: chain A8 residue 10 SER Chi-restraints excluded: chain BV residue 10 SER Chi-restraints excluded: chain BW residue 11 LYS Chi-restraints excluded: chain B0 residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 0.0060 chunk 107 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 0.0270 chunk 70 optimal weight: 0.0980 chunk 29 optimal weight: 0.0010 chunk 111 optimal weight: 3.9990 overall best weight: 0.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 2 HIS ** e 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.182590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.128111 restraints weight = 13277.697| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 4.10 r_work: 0.4043 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 10968 Z= 0.074 Angle : 0.490 3.865 13860 Z= 0.220 Chirality : 0.061 0.137 1386 Planarity : 0.004 0.035 1512 Dihedral : 8.738 63.345 2016 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.88 % Allowed : 16.77 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.25), residues: 1008 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR G 3 HIS 0.002 0.000 HISA6 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.07 (10710) covalent geometry : angle 0.49032 / 0.22 (13860) Misc. bond : bond 0.00017 / 0.01 ( 258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 TYR cc_start: 0.7489 (m-80) cc_final: 0.6092 (t80) REVERT: P 3 TYR cc_start: 0.7038 (m-80) cc_final: 0.6465 (m-10) REVERT: V 3 TYR cc_start: 0.7200 (m-80) cc_final: 0.6303 (t80) REVERT: Y 3 TYR cc_start: 0.7058 (m-80) cc_final: 0.5902 (p90) REVERT: 3 3 TYR cc_start: 0.7066 (m-80) cc_final: 0.5769 (p90) REVERT: 4 3 TYR cc_start: 0.6928 (m-80) cc_final: 0.6001 (t80) REVERT: 8 11 LYS cc_start: 0.8070 (mmtt) cc_final: 0.6015 (tmmm) REVERT: a 3 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.5832 (t80) REVERT: d 3 TYR cc_start: 0.7315 (m-80) cc_final: 0.6146 (t80) REVERT: m 11 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7783 (mptt) REVERT: v 3 TYR cc_start: 0.7536 (m-80) cc_final: 0.6239 (t80) REVERT: w 3 TYR cc_start: 0.7604 (OUTLIER) cc_final: 0.6847 (m-10) REVERT: y 3 TYR cc_start: 0.6892 (m-80) cc_final: 0.6148 (m-80) REVERT: AA 3 TYR cc_start: 0.6867 (m-80) cc_final: 0.6448 (m-80) REVERT: AE 3 TYR cc_start: 0.6446 (m-80) cc_final: 0.5790 (t80) REVERT: AF 3 TYR cc_start: 0.6755 (m-80) cc_final: 0.6451 (m-10) REVERT: AL 3 TYR cc_start: 0.7226 (m-80) cc_final: 0.6694 (t80) REVERT: AN 3 TYR cc_start: 0.7214 (m-80) cc_final: 0.5995 (t80) REVERT: AS 3 TYR cc_start: 0.6872 (m-80) cc_final: 0.6333 (m-80) REVERT: AT 3 TYR cc_start: 0.6857 (m-80) cc_final: 0.6144 (t80) REVERT: AW 11 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7880 (mptt) REVERT: AX 3 TYR cc_start: 0.6920 (m-80) cc_final: 0.6426 (m-10) REVERT: A5 3 TYR cc_start: 0.7471 (m-80) cc_final: 0.6302 (t80) REVERT: A8 3 TYR cc_start: 0.7017 (m-80) cc_final: 0.6443 (m-80) REVERT: BA 3 TYR cc_start: 0.6820 (m-10) cc_final: 0.6214 (m-10) REVERT: BB 3 TYR cc_start: 0.6511 (m-80) cc_final: 0.6044 (m-80) REVERT: BD 3 TYR cc_start: 0.7047 (m-80) cc_final: 0.6627 (m-80) REVERT: BE 3 TYR cc_start: 0.5861 (m-80) cc_final: 0.5297 (t80) REVERT: BI 11 LYS cc_start: 0.7648 (mmtt) cc_final: 0.6459 (mmtp) REVERT: BQ 3 TYR cc_start: 0.6858 (m-80) cc_final: 0.6368 (m-80) REVERT: BT 3 TYR cc_start: 0.6843 (m-80) cc_final: 0.6277 (t80) REVERT: BV 3 TYR cc_start: 0.6875 (m-80) cc_final: 0.6615 (m-80) REVERT: BW 3 TYR cc_start: 0.5873 (m-80) cc_final: 0.5297 (t80) outliers start: 19 outliers final: 12 residues processed: 131 average time/residue: 0.2399 time to fit residues: 37.4268 Evaluate side-chains 129 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain a residue 3 TYR Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain t residue 10 SER Chi-restraints excluded: chain w residue 3 TYR Chi-restraints excluded: chain z residue 10 SER Chi-restraints excluded: chain AW residue 10 SER Chi-restraints excluded: chain AW residue 11 LYS Chi-restraints excluded: chain A2 residue 10 SER Chi-restraints excluded: chain BW residue 11 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 2 HIS ** e 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.179841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.124605 restraints weight = 13465.022| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 4.16 r_work: 0.3989 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10968 Z= 0.157 Angle : 0.542 4.038 13860 Z= 0.241 Chirality : 0.062 0.134 1386 Planarity : 0.004 0.037 1512 Dihedral : 9.551 65.486 2016 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.79 % Allowed : 16.96 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.25), residues: 1008 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR k 3 HIS 0.003 0.000 HIS U 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (10710) covalent geometry : angle 0.54177 / 0.24 (13860) Misc. bond : bond 0.00066 / 0.04 ( 258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2989.32 seconds wall clock time: 51 minutes 58.49 seconds (3118.49 seconds total)