Starting phenix.real_space_refine on Wed Aug 5 03:11:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10sd_75431/08_2026/10sd_75431.cif Found real_map, /net/cci-nas-00/data/ceres_data/10sd_75431/08_2026/10sd_75431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10sd_75431/08_2026/10sd_75431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10sd_75431/08_2026/10sd_75431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10sd_75431/08_2026/10sd_75431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10sd_75431/08_2026/10sd_75431.map" } resolution = 3.11 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 5646 2.51 5 N 1344 2.21 5 O 1248 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: 8238 Number of models: 1 Model: "" Number of chains: 288 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: "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: "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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 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: "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: "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: "N" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 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: "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: "6" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 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: "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: "m" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 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: "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: "AC" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AD" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AE" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AF" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AG" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AH" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AI" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AJ" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AK" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AL" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AN" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AO" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AP" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AQ" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AR" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 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: "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: "AS" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AT" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AU" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AV" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AW" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AX" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AY" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AZ" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A0" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A1" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A2" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A3" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A4" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A5" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A6" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A7" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DKA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.43, per 1000 atoms: 0.29 Number of scatterers: 8238 At special positions: 0 Unit cell: (109.855, 101.205, 61.415, 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 1248 8.00 N 1344 7.00 C 5646 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=192, symmetry=0 Number of additional bonds: simple=192, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 341.9 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 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: 0.48 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: 0.00 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.27: 1056 1.27 - 1.34: 673 1.34 - 1.41: 1343 1.41 - 1.49: 1240 1.49 - 1.56: 3926 Bond restraints: 8238 Sorted by residual: bond pdb=" C SERAM 10 " pdb=" O SERAM 10 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" C SERA2 10 " pdb=" O SERA2 10 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.30e-02 5.92e+03 1.14e+01 bond pdb=" C SER w 10 " pdb=" O SER w 10 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" C SER g 10 " pdb=" O SER g 10 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" C SER L 10 " pdb=" O SER L 10 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.30e-02 5.92e+03 1.13e+01 ... (remaining 8233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 10035 3.55 - 7.09: 549 7.09 - 10.64: 36 10.64 - 14.18: 12 14.18 - 17.73: 6 Bond angle restraints: 10638 Sorted by residual: angle pdb=" C LYSAD 11 " pdb=" CA LYSAD 11 " pdb=" CB LYSAD 11 " ideal model delta sigma weight residual 110.10 122.37 -12.27 1.90e+00 2.77e-01 4.17e+01 angle pdb=" C LYS C 11 " pdb=" CA LYS C 11 " pdb=" CB LYS C 11 " ideal model delta sigma weight residual 110.10 122.35 -12.25 1.90e+00 2.77e-01 4.16e+01 angle pdb=" C LYS n 11 " pdb=" CA LYS n 11 " pdb=" CB LYS n 11 " ideal model delta sigma weight residual 110.10 122.33 -12.23 1.90e+00 2.77e-01 4.15e+01 angle pdb=" C LYS R 11 " pdb=" CA LYS R 11 " pdb=" CB LYS R 11 " ideal model delta sigma weight residual 110.10 122.33 -12.23 1.90e+00 2.77e-01 4.14e+01 angle pdb=" C LYS 7 11 " pdb=" CA LYS 7 11 " pdb=" CB LYS 7 11 " ideal model delta sigma weight residual 110.10 122.32 -12.22 1.90e+00 2.77e-01 4.14e+01 ... (remaining 10633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.96: 3918 11.96 - 23.91: 618 23.91 - 35.87: 144 35.87 - 47.83: 48 47.83 - 59.78: 54 Dihedral angle restraints: 4782 sinusoidal: 2286 harmonic: 2496 Sorted by residual: dihedral pdb=" C PRO l 4 " pdb=" N PRO l 4 " pdb=" CA PRO l 4 " pdb=" CB PRO l 4 " ideal model delta harmonic sigma weight residual -120.70 -128.99 8.29 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C PRO 5 4 " pdb=" N PRO 5 4 " pdb=" CA PRO 5 4 " pdb=" CB PRO 5 4 " ideal model delta harmonic sigma weight residual -120.70 -128.98 8.28 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C PROA7 4 " pdb=" N PROA7 4 " pdb=" CA PROA7 4 " pdb=" CB PROA7 4 " ideal model delta harmonic sigma weight residual -120.70 -128.96 8.26 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 4779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 519 0.073 - 0.146: 388 0.146 - 0.218: 83 0.218 - 0.291: 36 0.291 - 0.363: 30 Chirality restraints: 1056 Sorted by residual: chirality pdb=" CA PROAS 4 " pdb=" N PROAS 4 " pdb=" C PROAS 4 " pdb=" CB PROAS 4 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA PRO m 4 " pdb=" N PRO m 4 " pdb=" C PRO m 4 " pdb=" CB PRO m 4 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA PROAC 4 " pdb=" N PROAC 4 " pdb=" C PROAC 4 " pdb=" CB PROAC 4 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 1053 not shown) Planarity restraints: 1152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS h 2 " -0.042 2.00e-02 2.50e+03 3.45e-02 1.79e+01 pdb=" CG HIS h 2 " 0.056 2.00e-02 2.50e+03 pdb=" ND1 HIS h 2 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 HIS h 2 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS h 2 " -0.038 2.00e-02 2.50e+03 pdb=" NE2 HIS h 2 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS M 2 " -0.042 2.00e-02 2.50e+03 3.43e-02 1.77e+01 pdb=" CG HIS M 2 " 0.056 2.00e-02 2.50e+03 pdb=" ND1 HIS M 2 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 HIS M 2 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS M 2 " -0.038 2.00e-02 2.50e+03 pdb=" NE2 HIS M 2 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HISAN 2 " -0.042 2.00e-02 2.50e+03 3.43e-02 1.76e+01 pdb=" CG HISAN 2 " 0.056 2.00e-02 2.50e+03 pdb=" ND1 HISAN 2 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 HISAN 2 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HISAN 2 " -0.038 2.00e-02 2.50e+03 pdb=" NE2 HISAN 2 " -0.003 2.00e-02 2.50e+03 ... (remaining 1149 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 3838 3.01 - 3.48: 7524 3.48 - 3.95: 14304 3.95 - 4.43: 15648 4.43 - 4.90: 30669 Nonbonded interactions: 71983 Sorted by model distance: nonbonded pdb=" O SER k 10 " pdb=" OG SER k 10 " model vdw 2.536 3.040 nonbonded pdb=" O SERAA 10 " pdb=" OG SERAA 10 " model vdw 2.536 3.040 nonbonded pdb=" O SER Q 10 " pdb=" OG SER Q 10 " model vdw 2.536 3.040 nonbonded pdb=" O SERAQ 10 " pdb=" OG SERAQ 10 " model vdw 2.536 3.040 nonbonded pdb=" O SER 4 10 " pdb=" OG SER 4 10 " model vdw 2.536 3.040 ... (remaining 71978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain '1' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain '2' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain '3' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain '4' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain '5' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain '6' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain '7' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain '8' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain '9' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'A' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'A0' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'A1' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'A2' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'A3' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'A4' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'A5' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'A6' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'A7' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AA' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AB' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AC' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AD' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AE' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AF' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AG' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AH' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = chain 'AI' selection = (chain 'AJ' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AK' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AL' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AM' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AN' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AO' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AP' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AQ' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AR' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AS' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AT' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AU' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AV' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AW' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'AX' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = chain 'AY' selection = (chain 'AZ' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or nam \ e O1 )))) selection = (chain 'B' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'C' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'D' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'E' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'F' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'G' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = chain 'H' selection = (chain 'I' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'J' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'K' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'L' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'M' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'N' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'O' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'P' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'Q' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'R' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'S' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'T' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'U' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'V' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = chain 'W' selection = (chain 'X' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'Y' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'Z' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'a' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'b' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = chain 'c' selection = (chain 'd' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'e' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'f' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'g' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'h' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'i' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'j' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'k' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'l' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'm' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'n' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'o' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'p' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'q' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'r' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = chain 's' selection = (chain 't' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'u' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'v' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'w' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'x' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'y' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) selection = (chain 'z' and (resid 2 through 12 or (resid 101 and (name C1 or name C2 or name \ O1 )))) } 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: 2.530 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.230 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 0.192 8430 Z= 2.236 Angle : 1.890 17.726 10638 Z= 1.086 Chirality : 0.112 0.363 1056 Planarity : 0.010 0.035 1152 Dihedral : 13.705 59.785 3246 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.31 % Favored : 79.69 % Rotamer: Outliers : 2.34 % Allowed : 3.91 % Favored : 93.75 % Cbeta Deviations : 0.78 % 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: -5.92 (0.21), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.041 0.005 TYR u 3 HIS 0.022 0.004 HIS h 2 Details of bonding type rmsd/Z covalent geometry : bond 0.01258 / 0.73 ( 8238) covalent geometry : angle 1.89038 / 1.09 (10638) Misc. bond : bond 0.14031 / 10.03 ( 192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 11 LYS cc_start: 0.5765 (OUTLIER) cc_final: 0.4870 (ttpt) REVERT: 5 3 TYR cc_start: 0.7010 (m-80) cc_final: 0.6772 (p90) REVERT: AI 2 HIS cc_start: 0.3236 (m90) cc_final: 0.2794 (t-170) REVERT: A7 11 LYS cc_start: 0.8087 (mttt) cc_final: 0.7704 (mptt) outliers start: 18 outliers final: 6 residues processed: 91 average time/residue: 0.0962 time to fit residues: 12.4180 Evaluate side-chains 69 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain 2 residue 11 LYS Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain q residue 10 SER Chi-restraints excluded: chain AG residue 10 SER Chi-restraints excluded: chain AW residue 10 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 2 HIS H 2 HIS I 2 HIS M 2 HIS O 2 HIS W 2 HIS 1 2 HIS b 2 HIS c 2 HIS ** d 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 2 HIS i 2 HIS r 2 HIS s 2 HIS t 2 HIS x 2 HIS y 2 HIS AH 2 HIS AJ 2 HIS AN 2 HIS AO 2 HIS AP 2 HIS AX 2 HIS AZ 2 HIS A3 2 HIS A4 2 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.200859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.156787 restraints weight = 9939.795| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 4.85 r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8430 Z= 0.127 Angle : 0.619 5.017 10638 Z= 0.268 Chirality : 0.063 0.140 1056 Planarity : 0.004 0.041 1152 Dihedral : 10.687 59.483 1624 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 1.82 % Allowed : 7.42 % Favored : 90.76 % 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: -5.75 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR e 3 HIS 0.009 0.001 HIS d 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 8238) covalent geometry : angle 0.61920 / 0.27 (10638) Misc. bond : bond 0.00065 / 0.05 ( 192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 11 LYS cc_start: 0.5687 (OUTLIER) cc_final: 0.4343 (tmtt) REVERT: A7 11 LYS cc_start: 0.7491 (mttt) cc_final: 0.6773 (mptt) outliers start: 14 outliers final: 7 residues processed: 95 average time/residue: 0.0919 time to fit residues: 12.6036 Evaluate side-chains 70 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain 2 residue 11 LYS Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain l residue 5 ILE Chi-restraints excluded: chain p residue 7 ILE Chi-restraints excluded: chain AB residue 5 ILE Chi-restraints excluded: chain AJ residue 2 HIS Chi-restraints excluded: chain AZ residue 2 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 93 optimal weight: 0.0010 chunk 27 optimal weight: 5.9990 overall best weight: 4.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 2 HIS I 2 HIS J 2 HIS ** L 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 HIS ** 0 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 2 HIS ** 9 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 2 HIS ** d 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 2 HIS u 2 HIS AJ 2 HIS AK 2 HIS ** AM 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AZ 2 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.193095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.146791 restraints weight = 10266.219| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 4.80 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.071 8430 Z= 0.415 Angle : 0.972 7.860 10638 Z= 0.454 Chirality : 0.074 0.166 1056 Planarity : 0.008 0.057 1152 Dihedral : 15.236 59.219 1618 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.83 % Favored : 76.17 % Rotamer: Outliers : 1.56 % Allowed : 13.54 % Favored : 84.90 % 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: -5.92 (0.21), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.003 TYRAJ 3 HIS 0.015 0.001 HISAZ 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00976 / 0.42 ( 8238) covalent geometry : angle 0.97154 / 0.45 (10638) Misc. bond : bond 0.00172 / 0.12 ( 192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 3 TYR cc_start: 0.5498 (m-80) cc_final: 0.4698 (p90) REVERT: b 3 TYR cc_start: 0.6127 (m-80) cc_final: 0.5883 (m-10) REVERT: AG 5 ILE cc_start: 0.8531 (mt) cc_final: 0.8259 (mp) REVERT: AI 2 HIS cc_start: 0.3855 (t-170) cc_final: 0.3434 (t-170) REVERT: A7 11 LYS cc_start: 0.8136 (mttt) cc_final: 0.7570 (mptt) outliers start: 12 outliers final: 8 residues processed: 92 average time/residue: 0.0735 time to fit residues: 10.1940 Evaluate side-chains 78 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain l residue 5 ILE Chi-restraints excluded: chain t residue 2 HIS Chi-restraints excluded: chain AB residue 5 ILE Chi-restraints excluded: chain AJ residue 2 HIS Chi-restraints excluded: chain AZ residue 2 HIS Chi-restraints excluded: chain A7 residue 5 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 2 HIS ** X 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 2 HIS ** AZ 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.202935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.154694 restraints weight = 10153.794| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 4.98 r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8430 Z= 0.123 Angle : 0.598 5.292 10638 Z= 0.264 Chirality : 0.061 0.146 1056 Planarity : 0.006 0.043 1152 Dihedral : 11.771 59.965 1614 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 1.17 % Allowed : 15.89 % Favored : 82.94 % 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: -5.66 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR M 3 HIS 0.010 0.001 HISAJ 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 ( 8238) covalent geometry : angle 0.59777 / 0.26 (10638) Misc. bond : bond 0.00046 / 0.03 ( 192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 2 HIS cc_start: 0.4777 (t-90) cc_final: 0.4411 (t-170) REVERT: AI 2 HIS cc_start: 0.3501 (t-170) cc_final: 0.3130 (t-170) REVERT: A7 11 LYS cc_start: 0.7963 (mttt) cc_final: 0.7162 (mptt) outliers start: 9 outliers final: 4 residues processed: 79 average time/residue: 0.0576 time to fit residues: 6.9893 Evaluate side-chains 65 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 3 TYR Chi-restraints excluded: chain p residue 7 ILE Chi-restraints excluded: chain z residue 5 ILE Chi-restraints excluded: chain AV residue 7 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 2 HIS ** 9 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AZ 2 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.194753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.140981 restraints weight = 11445.641| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 5.56 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8430 Z= 0.249 Angle : 0.748 9.475 10638 Z= 0.338 Chirality : 0.066 0.173 1056 Planarity : 0.006 0.048 1152 Dihedral : 12.822 59.588 1614 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.57 % Favored : 79.43 % Rotamer: Outliers : 1.82 % Allowed : 16.93 % 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: -5.59 (0.21), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.26 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR F 3 HIS 0.004 0.001 HIS P 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 ( 8238) covalent geometry : angle 0.74843 / 0.34 (10638) Misc. bond : bond 0.00112 / 0.07 ( 192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 2 HIS cc_start: 0.4447 (t-90) cc_final: 0.4215 (t-170) REVERT: w 2 HIS cc_start: 0.3299 (m-70) cc_final: 0.2721 (m90) REVERT: A2 2 HIS cc_start: 0.4231 (m-70) cc_final: 0.3214 (p90) REVERT: A7 11 LYS cc_start: 0.7995 (mttt) cc_final: 0.7233 (mptt) outliers start: 14 outliers final: 9 residues processed: 83 average time/residue: 0.0496 time to fit residues: 6.4615 Evaluate side-chains 73 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain F residue 3 TYR Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain U residue 3 TYR Chi-restraints excluded: chain e residue 3 TYR Chi-restraints excluded: chain j residue 10 SER Chi-restraints excluded: chain AL residue 10 SER Chi-restraints excluded: chain A1 residue 10 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 HIS ** 9 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 HIS AZ 2 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.198155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.148855 restraints weight = 11261.093| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 5.15 r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 8430 Z= 0.313 Angle : 0.801 5.617 10638 Z= 0.372 Chirality : 0.070 0.190 1056 Planarity : 0.007 0.051 1152 Dihedral : 13.427 59.847 1614 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.57 % Favored : 79.43 % Rotamer: Outliers : 4.30 % Allowed : 17.71 % Favored : 77.99 % 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: -5.56 (0.22), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.002 TYR q 3 HIS 0.004 0.001 HIS 1 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.32 ( 8238) covalent geometry : angle 0.80088 / 0.37 (10638) Misc. bond : bond 0.00121 / 0.08 ( 192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 SER cc_start: 0.7248 (OUTLIER) cc_final: 0.6824 (t) REVERT: W 2 HIS cc_start: 0.4472 (t-90) cc_final: 0.4145 (t-170) REVERT: 4 3 TYR cc_start: 0.6267 (OUTLIER) cc_final: 0.4533 (p90) REVERT: o 10 SER cc_start: 0.7294 (OUTLIER) cc_final: 0.7050 (t) REVERT: AR 2 HIS cc_start: 0.2621 (m-70) cc_final: 0.2360 (m170) REVERT: AT 3 TYR cc_start: 0.5638 (OUTLIER) cc_final: 0.5156 (t80) REVERT: A7 11 LYS cc_start: 0.8277 (mttt) cc_final: 0.7449 (mptt) outliers start: 33 outliers final: 24 residues processed: 100 average time/residue: 0.0515 time to fit residues: 8.0193 Evaluate side-chains 98 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain F residue 3 TYR Chi-restraints excluded: chain M residue 3 TYR Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain U residue 2 HIS Chi-restraints excluded: chain U residue 3 TYR Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain a residue 3 TYR Chi-restraints excluded: chain e residue 3 TYR Chi-restraints excluded: chain j residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain l residue 5 ILE Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain o residue 10 SER Chi-restraints excluded: chain q residue 3 TYR Chi-restraints excluded: chain AB residue 5 ILE Chi-restraints excluded: chain AC residue 10 SER Chi-restraints excluded: chain AG residue 3 TYR Chi-restraints excluded: chain AL residue 10 SER Chi-restraints excluded: chain AN residue 3 TYR Chi-restraints excluded: chain AS residue 10 SER Chi-restraints excluded: chain AT residue 3 TYR Chi-restraints excluded: chain AW residue 3 TYR Chi-restraints excluded: chain AZ residue 2 HIS Chi-restraints excluded: chain A1 residue 10 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 31 optimal weight: 0.0970 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 2 HIS ** T 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 HIS ** 9 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 2 HIS t 2 HIS AZ 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.202699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.153437 restraints weight = 10681.763| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 5.07 r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8430 Z= 0.150 Angle : 0.619 4.923 10638 Z= 0.278 Chirality : 0.063 0.145 1056 Planarity : 0.006 0.062 1152 Dihedral : 11.695 58.388 1614 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.10 % Favored : 81.90 % Rotamer: Outliers : 2.73 % Allowed : 19.40 % Favored : 77.86 % 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: -5.44 (0.21), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR q 3 HIS 0.017 0.001 HIS U 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 8238) covalent geometry : angle 0.61868 / 0.28 (10638) Misc. bond : bond 0.00055 / 0.04 ( 192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 2 HIS cc_start: 0.4502 (t-90) cc_final: 0.4245 (t-170) REVERT: 4 3 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.4275 (p90) REVERT: l 3 TYR cc_start: 0.6124 (OUTLIER) cc_final: 0.5778 (m-10) REVERT: o 10 SER cc_start: 0.7228 (OUTLIER) cc_final: 0.6952 (t) REVERT: AD 3 TYR cc_start: 0.4890 (OUTLIER) cc_final: 0.4588 (t80) REVERT: AT 3 TYR cc_start: 0.5678 (OUTLIER) cc_final: 0.4806 (t80) REVERT: A7 11 LYS cc_start: 0.8249 (mttt) cc_final: 0.7416 (mptt) outliers start: 21 outliers final: 11 residues processed: 94 average time/residue: 0.0560 time to fit residues: 8.2614 Evaluate side-chains 86 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 3 TYR Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain U residue 3 TYR Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain o residue 10 SER Chi-restraints excluded: chain AB residue 5 ILE Chi-restraints excluded: chain AD residue 3 TYR Chi-restraints excluded: chain AL residue 10 SER Chi-restraints excluded: chain AN residue 3 TYR Chi-restraints excluded: chain AT residue 3 TYR Chi-restraints excluded: chain A1 residue 10 SER Chi-restraints excluded: chain A7 residue 5 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 2 HIS ** T 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 HIS AA 2 HIS AB 2 HIS AR 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.195705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.143050 restraints weight = 10506.614| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 5.31 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8430 Z= 0.228 Angle : 0.707 6.080 10638 Z= 0.326 Chirality : 0.066 0.161 1056 Planarity : 0.007 0.070 1152 Dihedral : 11.985 59.140 1614 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.27 % Favored : 77.73 % Rotamer: Outliers : 3.91 % Allowed : 19.66 % Favored : 76.43 % 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: -5.34 (0.22), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR q 3 HIS 0.005 0.001 HIS 5 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 ( 8238) covalent geometry : angle 0.70703 / 0.33 (10638) Misc. bond : bond 0.00085 / 0.06 ( 192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 SER cc_start: 0.7334 (OUTLIER) cc_final: 0.6789 (t) REVERT: A 10 SER cc_start: 0.8449 (m) cc_final: 0.7193 (p) REVERT: W 2 HIS cc_start: 0.4518 (t-90) cc_final: 0.4267 (t-170) REVERT: 4 3 TYR cc_start: 0.6123 (OUTLIER) cc_final: 0.4244 (p90) REVERT: 8 10 SER cc_start: 0.7167 (OUTLIER) cc_final: 0.6748 (t) REVERT: e 3 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.6517 (t80) REVERT: o 10 SER cc_start: 0.7401 (OUTLIER) cc_final: 0.6930 (t) REVERT: AD 3 TYR cc_start: 0.5061 (OUTLIER) cc_final: 0.4589 (t80) REVERT: AE 10 SER cc_start: 0.6681 (OUTLIER) cc_final: 0.6340 (t) REVERT: AT 3 TYR cc_start: 0.5750 (OUTLIER) cc_final: 0.4801 (t80) REVERT: A2 3 TYR cc_start: 0.6331 (m-80) cc_final: 0.4838 (m-80) REVERT: A7 11 LYS cc_start: 0.8216 (mttt) cc_final: 0.7378 (mptt) outliers start: 30 outliers final: 20 residues processed: 98 average time/residue: 0.0496 time to fit residues: 7.5089 Evaluate side-chains 103 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain M residue 3 TYR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain U residue 2 HIS Chi-restraints excluded: chain U residue 3 TYR Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 8 residue 10 SER Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain a residue 3 TYR Chi-restraints excluded: chain e residue 3 TYR Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain o residue 10 SER Chi-restraints excluded: chain q residue 3 TYR Chi-restraints excluded: chain AB residue 5 ILE Chi-restraints excluded: chain AC residue 10 SER Chi-restraints excluded: chain AD residue 3 TYR Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AG residue 3 TYR Chi-restraints excluded: chain AL residue 10 SER Chi-restraints excluded: chain AN residue 3 TYR Chi-restraints excluded: chain AR residue 2 HIS Chi-restraints excluded: chain AT residue 3 TYR Chi-restraints excluded: chain AW residue 3 TYR Chi-restraints excluded: chain AZ residue 2 HIS Chi-restraints excluded: chain A7 residue 3 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 0.4980 chunk 93 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 2 HIS ** T 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.198746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.145775 restraints weight = 10602.619| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 5.34 r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8430 Z= 0.137 Angle : 0.605 4.978 10638 Z= 0.275 Chirality : 0.062 0.144 1056 Planarity : 0.007 0.062 1152 Dihedral : 10.623 59.923 1614 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % Rotamer: Outliers : 3.26 % Allowed : 20.31 % Favored : 76.43 % 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: -5.31 (0.21), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.044 0.002 TYR A 3 HIS 0.007 0.001 HISAR 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 8238) covalent geometry : angle 0.60547 / 0.27 (10638) Misc. bond : bond 0.00046 / 0.03 ( 192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 SER cc_start: 0.8464 (m) cc_final: 0.7296 (p) REVERT: W 2 HIS cc_start: 0.4541 (t-90) cc_final: 0.4317 (t-170) REVERT: 4 3 TYR cc_start: 0.5843 (OUTLIER) cc_final: 0.3963 (p90) REVERT: 8 10 SER cc_start: 0.7194 (OUTLIER) cc_final: 0.6973 (t) REVERT: e 3 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.6321 (t80) REVERT: l 3 TYR cc_start: 0.6152 (OUTLIER) cc_final: 0.5621 (m-10) REVERT: AD 3 TYR cc_start: 0.5074 (OUTLIER) cc_final: 0.4867 (t80) REVERT: AT 3 TYR cc_start: 0.5846 (OUTLIER) cc_final: 0.5014 (t80) REVERT: A2 3 TYR cc_start: 0.6176 (m-80) cc_final: 0.4836 (m-80) REVERT: A7 11 LYS cc_start: 0.8198 (mttt) cc_final: 0.7396 (mptt) outliers start: 25 outliers final: 15 residues processed: 95 average time/residue: 0.0523 time to fit residues: 7.6612 Evaluate side-chains 95 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 TYR Chi-restraints excluded: chain M residue 3 TYR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain U residue 2 HIS Chi-restraints excluded: chain U residue 3 TYR Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 8 residue 10 SER Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain e residue 3 TYR Chi-restraints excluded: chain j residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain p residue 7 ILE Chi-restraints excluded: chain AB residue 3 TYR Chi-restraints excluded: chain AB residue 5 ILE Chi-restraints excluded: chain AC residue 10 SER Chi-restraints excluded: chain AD residue 3 TYR Chi-restraints excluded: chain AN residue 3 TYR Chi-restraints excluded: chain AT residue 3 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 94 optimal weight: 0.0020 chunk 89 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.196103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.143528 restraints weight = 10504.962| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 5.33 r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8430 Z= 0.201 Angle : 0.673 5.071 10638 Z= 0.309 Chirality : 0.064 0.141 1056 Planarity : 0.007 0.073 1152 Dihedral : 10.881 59.524 1614 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.96 % Favored : 79.04 % Rotamer: Outliers : 3.26 % Allowed : 20.70 % Favored : 76.04 % 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: -5.27 (0.21), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.043 0.002 TYRAB 3 HIS 0.007 0.001 HISAR 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 ( 8238) covalent geometry : angle 0.67336 / 0.31 (10638) Misc. bond : bond 0.00074 / 0.05 ( 192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 SER cc_start: 0.8507 (m) cc_final: 0.7302 (p) REVERT: 4 3 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.4002 (p90) REVERT: 8 10 SER cc_start: 0.7220 (OUTLIER) cc_final: 0.6945 (t) REVERT: e 3 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.6319 (t80) REVERT: l 3 TYR cc_start: 0.5806 (OUTLIER) cc_final: 0.5398 (m-10) REVERT: AD 3 TYR cc_start: 0.5316 (OUTLIER) cc_final: 0.4817 (t80) REVERT: AT 3 TYR cc_start: 0.5849 (OUTLIER) cc_final: 0.4917 (t80) REVERT: A2 3 TYR cc_start: 0.6200 (m-80) cc_final: 0.4914 (m-80) REVERT: A7 11 LYS cc_start: 0.8273 (mttt) cc_final: 0.7470 (mptt) outliers start: 25 outliers final: 18 residues processed: 92 average time/residue: 0.0530 time to fit residues: 7.5106 Evaluate side-chains 96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 TYR Chi-restraints excluded: chain M residue 3 TYR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain U residue 2 HIS Chi-restraints excluded: chain U residue 3 TYR Chi-restraints excluded: chain 4 residue 3 TYR Chi-restraints excluded: chain 8 residue 10 SER Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain a residue 3 TYR Chi-restraints excluded: chain e residue 3 TYR Chi-restraints excluded: chain j residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain o residue 10 SER Chi-restraints excluded: chain t residue 2 HIS Chi-restraints excluded: chain AB residue 3 TYR Chi-restraints excluded: chain AB residue 5 ILE Chi-restraints excluded: chain AC residue 10 SER Chi-restraints excluded: chain AD residue 3 TYR Chi-restraints excluded: chain AN residue 3 TYR Chi-restraints excluded: chain AS residue 10 SER Chi-restraints excluded: chain AT residue 3 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 0.0970 overall best weight: 4.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 2 HIS ** 9 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 HIS AC 2 HIS AX 2 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.194438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.146338 restraints weight = 10618.942| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 4.94 r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 8430 Z= 0.377 Angle : 0.882 5.853 10638 Z= 0.418 Chirality : 0.073 0.163 1056 Planarity : 0.007 0.063 1152 Dihedral : 12.855 59.646 1614 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.65 % Favored : 74.35 % Rotamer: Outliers : 4.17 % Allowed : 19.79 % Favored : 76.04 % 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: -5.40 (0.22), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.17), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.032 0.003 TYRAB 3 HIS 0.008 0.001 HIS t 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00877 / 0.38 ( 8238) covalent geometry : angle 0.88163 / 0.42 (10638) Misc. bond : bond 0.00144 / 0.10 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1258.27 seconds wall clock time: 22 minutes 36.52 seconds (1356.52 seconds total)