Starting phenix.real_space_refine on Thu Aug 6 01:15:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10sf_75433/08_2026/10sf_75433.cif Found real_map, /net/cci-nas-00/data/ceres_data/10sf_75433/08_2026/10sf_75433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10sf_75433/08_2026/10sf_75433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10sf_75433/08_2026/10sf_75433.map" model { file = "/net/cci-nas-00/data/ceres_data/10sf_75433/08_2026/10sf_75433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10sf_75433/08_2026/10sf_75433.cif" } resolution = 3.08 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 8640 2.51 5 N 2016 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.01s 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: 12528 Number of models: 1 Model: "" Number of chains: 432 Chain: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "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: "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: "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: "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: 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: 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 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: 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: "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: 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 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: "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: 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: 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: 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AC" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AE" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AF" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AG" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AI" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 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: 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: 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: 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: "AH" 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: "AI" 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: "AJ" 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: "AK" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AM" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AO" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AQ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AS" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AS" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AT" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AU" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AV" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AW" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AX" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AY" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AY" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AZ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "AZ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AK" Number of atoms: 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: 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: 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: "AX" 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: "AY" 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: "AZ" 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: "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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A3" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A4" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A5" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A6" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A7" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A8" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A9" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BC" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BD" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BE" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BF" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BG" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BH" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BI" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BJ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A2" Number of atoms: 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 Chain: "A8" 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: "A9" 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: "BA" 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: "BB" 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: "BC" 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: "BD" 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: "BE" 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: "BF" 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: "BG" 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: "BH" 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: "BI" 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: "BJ" 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: "BK" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BL" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BM" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BN" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BO" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BP" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BQ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BR" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BS" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BS" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BT" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BU" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BV" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BW" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BX" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BY" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BY" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BZ" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "BZ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "BK" Number of atoms: 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: "BL" 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: "BM" 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: "BN" 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: "BO" 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: "BP" 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: "BQ" 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: "BR" 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: "BS" 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: "BT" 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: "BU" 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: "BV" 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: "BW" 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: "BX" 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: "BY" 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: "BZ" 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: "B0" 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: "B1" 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: "B2" 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: "B2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B3" 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: "B3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B4" 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: "B4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B5" 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: "B5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B6" 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: "B6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B7" 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: "B7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B8" 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: "B8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B9" 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: "B9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "CA" 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: "CA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "CB" 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: "CB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "CC" 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: "CC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "CD" 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: "CD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "CE" 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: "CE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "CF" 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: "CF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "CG" 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: "CG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "CH" 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: "CH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "CI" 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: "CI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "CJ" 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: "CJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B2" 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: "B3" 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: "B4" 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: "B5" 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: "B6" 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: "B7" 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: "B8" 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: "B9" 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: "CA" 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: "CB" 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: "CC" 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: "CD" 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: "CE" 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: "CF" 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: "CG" 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: "CH" 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: "CI" 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: "CJ" 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: 4.16, per 1000 atoms: 0.33 Number of scatterers: 12528 At special positions: 0 Unit cell: (117.64, 108.125, 70.065, 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 1872 8.00 N 2016 7.00 C 8640 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=288, symmetry=0 Number of additional bonds: simple=288, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 431.4 milliseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 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: 0.57 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: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.26: 1584 1.26 - 1.34: 636 1.34 - 1.41: 2388 1.41 - 1.49: 1822 1.49 - 1.56: 6098 Bond restraints: 12528 Sorted by residual: bond pdb=" C1 DKABA 101 " pdb=" O1 DKABA 101 " ideal model delta sigma weight residual 1.247 1.187 0.060 2.00e-02 2.50e+03 9.08e+00 bond pdb=" C1 DKA 0 101 " pdb=" O1 DKA 0 101 " ideal model delta sigma weight residual 1.247 1.187 0.060 2.00e-02 2.50e+03 9.07e+00 bond pdb=" C1 DKACA 101 " pdb=" O1 DKACA 101 " ideal model delta sigma weight residual 1.247 1.187 0.060 2.00e-02 2.50e+03 9.05e+00 bond pdb=" C1 DKABS 101 " pdb=" O1 DKABS 101 " ideal model delta sigma weight residual 1.247 1.187 0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" C1 DKA I 101 " pdb=" O1 DKA I 101 " ideal model delta sigma weight residual 1.247 1.187 0.060 2.00e-02 2.50e+03 9.02e+00 ... (remaining 12523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 13647 2.42 - 4.84: 2143 4.84 - 7.26: 248 7.26 - 9.68: 82 9.68 - 12.10: 8 Bond angle restraints: 16128 Sorted by residual: angle pdb=" C LYSBD 11 " pdb=" CA LYSBD 11 " pdb=" CB LYSBD 11 " ideal model delta sigma weight residual 110.10 118.28 -8.18 1.90e+00 2.77e-01 1.85e+01 angle pdb=" C LYSBV 11 " pdb=" CA LYSBV 11 " pdb=" CB LYSBV 11 " ideal model delta sigma weight residual 110.10 118.28 -8.18 1.90e+00 2.77e-01 1.85e+01 angle pdb=" C LYS l 11 " pdb=" CA LYS l 11 " pdb=" CB LYS l 11 " ideal model delta sigma weight residual 110.10 118.28 -8.18 1.90e+00 2.77e-01 1.85e+01 angle pdb=" C LYS 3 11 " pdb=" CA LYS 3 11 " pdb=" CB LYS 3 11 " ideal model delta sigma weight residual 110.10 118.28 -8.18 1.90e+00 2.77e-01 1.85e+01 angle pdb=" C LYSCD 11 " pdb=" CA LYSCD 11 " pdb=" CB LYSCD 11 " ideal model delta sigma weight residual 110.10 118.27 -8.17 1.90e+00 2.77e-01 1.85e+01 ... (remaining 16123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 6284 11.82 - 23.64: 836 23.64 - 35.46: 160 35.46 - 47.28: 32 47.28 - 59.10: 32 Dihedral angle restraints: 7344 sinusoidal: 3600 harmonic: 3744 Sorted by residual: dihedral pdb=" CA GLYAL 9 " pdb=" C GLYAL 9 " pdb=" N SERAL 10 " pdb=" CA SERAL 10 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLYB3 9 " pdb=" C GLYB3 9 " pdb=" N SERB3 10 " pdb=" CA SERB3 10 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLY t 9 " pdb=" C GLY t 9 " pdb=" N SER t 10 " pdb=" CA SER t 10 " ideal model delta harmonic sigma weight residual 180.00 -160.05 -19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 7341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 693 0.061 - 0.122: 592 0.122 - 0.184: 187 0.184 - 0.245: 64 0.245 - 0.306: 48 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA PROBT 4 " pdb=" N PROBT 4 " pdb=" C PROBT 4 " pdb=" CB PROBT 4 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA PROCB 4 " pdb=" N PROCB 4 " pdb=" C PROCB 4 " pdb=" CB PROCB 4 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA PRO 1 4 " pdb=" N PRO 1 4 " pdb=" C PRO 1 4 " pdb=" CB PRO 1 4 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 1581 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRCH 3 " 0.039 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYRCH 3 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYRCH 3 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYRCH 3 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYRCH 3 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYRCH 3 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYRCH 3 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYRCH 3 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR p 3 " 0.039 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR p 3 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR p 3 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR p 3 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR p 3 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR p 3 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR p 3 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR p 3 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRAH 3 " 0.039 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYRAH 3 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYRAH 3 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYRAH 3 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYRAH 3 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYRAH 3 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYRAH 3 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYRAH 3 " 0.041 2.00e-02 2.50e+03 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 907 2.77 - 3.31: 11311 3.31 - 3.84: 19872 3.84 - 4.37: 28008 4.37 - 4.90: 50458 Nonbonded interactions: 110556 Sorted by model distance: nonbonded pdb=" C9 DKAA2 101 " pdb=" C10 DKABY 101 " model vdw 2.242 3.860 nonbonded pdb=" C9 DKA S 101 " pdb=" C10 DKA o 101 " model vdw 2.242 3.860 nonbonded pdb=" C9 DKABK 101 " pdb=" C10 DKACG 101 " model vdw 2.242 3.860 nonbonded pdb=" C9 DKA s 101 " pdb=" C10 DKAAY 101 " model vdw 2.242 3.860 nonbonded pdb=" C10 DKA O 101 " pdb=" C9 DKAAK 101 " model vdw 2.242 3.860 ... (remaining 110551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'A0' selection = chain 'A1' selection = chain 'A2' selection = chain 'A3' selection = chain 'A4' selection = chain 'A5' selection = chain 'A6' selection = chain 'A7' selection = chain 'A8' selection = chain 'A9' selection = chain 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'AE' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'AI' selection = chain 'AJ' selection = chain 'AK' selection = chain 'AL' selection = chain 'AM' selection = chain 'AN' selection = chain 'AO' selection = chain 'AP' selection = chain 'AQ' selection = chain 'AR' selection = chain 'AS' selection = chain 'AT' selection = chain 'AU' selection = chain 'AV' selection = chain 'AW' selection = chain 'AX' selection = chain 'AY' selection = chain 'AZ' selection = chain 'B' selection = chain 'B0' selection = chain 'B1' selection = chain 'B2' selection = chain 'B3' selection = chain 'B4' selection = chain 'B5' selection = chain 'B6' selection = chain 'B7' selection = chain 'B8' selection = chain 'B9' selection = chain 'BA' selection = chain 'BB' selection = chain 'BC' selection = chain 'BD' selection = chain 'BE' selection = chain 'BF' selection = chain 'BG' selection = chain 'BH' selection = chain 'BI' selection = chain 'BJ' selection = chain 'BK' selection = chain 'BL' selection = chain 'BM' selection = chain 'BN' selection = chain 'BO' selection = chain 'BP' selection = chain 'BQ' selection = chain 'BR' selection = chain 'BS' selection = chain 'BT' selection = chain 'BU' selection = chain 'BV' selection = chain 'BW' selection = chain 'BX' selection = chain 'BY' selection = chain 'BZ' selection = chain 'C' selection = chain 'CA' selection = chain 'CB' selection = chain 'CC' selection = chain 'CD' selection = chain 'CE' selection = chain 'CF' selection = chain 'CG' selection = chain 'CH' selection = chain 'CI' selection = chain 'CJ' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.600 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 0.200 12816 Z= 2.255 Angle : 1.874 12.096 16128 Z= 1.053 Chirality : 0.101 0.306 1584 Planarity : 0.009 0.026 1728 Dihedral : 11.006 59.097 5040 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 1.39 % Allowed : 4.17 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.20 (0.20), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.041 0.006 TYRAH 3 HIS 0.025 0.004 HISBJ 2 Details of bonding type rmsd/Z covalent geometry : bond 0.01290 / 0.74 (12528) covalent geometry : angle 1.87364 / 1.05 (16128) Misc. bond : bond 0.14227 / 9.69 ( 288) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 225 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 SER cc_start: 0.8874 (p) cc_final: 0.8656 (t) REVERT: G 10 SER cc_start: 0.8985 (p) cc_final: 0.8727 (p) REVERT: M 3 TYR cc_start: 0.6518 (m-80) cc_final: 0.6088 (m-80) REVERT: O 3 TYR cc_start: 0.6385 (m-80) cc_final: 0.6022 (m-80) REVERT: P 3 TYR cc_start: 0.7333 (m-80) cc_final: 0.6942 (m-80) REVERT: Q 3 TYR cc_start: 0.6618 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: Q 10 SER cc_start: 0.9212 (p) cc_final: 0.8821 (p) REVERT: R 3 TYR cc_start: 0.6822 (m-80) cc_final: 0.6505 (m-80) REVERT: X 11 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7675 (tmtt) REVERT: Z 3 TYR cc_start: 0.7374 (m-80) cc_final: 0.6597 (p90) REVERT: 0 3 TYR cc_start: 0.7465 (m-80) cc_final: 0.6933 (m-80) REVERT: 0 11 LYS cc_start: 0.7943 (mmtt) cc_final: 0.6312 (tttm) REVERT: 2 11 LYS cc_start: 0.6948 (ttmt) cc_final: 0.5625 (tmtt) REVERT: 4 3 TYR cc_start: 0.7023 (m-80) cc_final: 0.5775 (p90) REVERT: 6 3 TYR cc_start: 0.6854 (m-80) cc_final: 0.6496 (m-80) REVERT: 6 11 LYS cc_start: 0.7857 (mttt) cc_final: 0.6664 (tttm) REVERT: 7 3 TYR cc_start: 0.8130 (m-80) cc_final: 0.7616 (m-80) REVERT: 8 3 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.5815 (p90) REVERT: 8 10 SER cc_start: 0.9000 (p) cc_final: 0.8794 (p) REVERT: g 10 SER cc_start: 0.8684 (p) cc_final: 0.8408 (p) REVERT: i 3 TYR cc_start: 0.6586 (m-80) cc_final: 0.6190 (m-80) REVERT: m 3 TYR cc_start: 0.6738 (m-80) cc_final: 0.6007 (m-10) REVERT: o 3 TYR cc_start: 0.6285 (m-80) cc_final: 0.6076 (m-80) REVERT: p 3 TYR cc_start: 0.7298 (m-80) cc_final: 0.6859 (m-80) REVERT: q 10 SER cc_start: 0.9256 (p) cc_final: 0.8936 (p) REVERT: r 3 TYR cc_start: 0.6857 (m-80) cc_final: 0.6607 (m-80) REVERT: y 10 SER cc_start: 0.8814 (p) cc_final: 0.8557 (p) REVERT: AA 3 TYR cc_start: 0.6542 (m-80) cc_final: 0.6194 (m-80) REVERT: AE 3 TYR cc_start: 0.6571 (m-80) cc_final: 0.6115 (m-80) REVERT: AG 3 TYR cc_start: 0.6088 (m-80) cc_final: 0.5886 (m-80) REVERT: AH 3 TYR cc_start: 0.7217 (m-80) cc_final: 0.6729 (m-80) REVERT: AI 3 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.6115 (m-80) REVERT: AI 10 SER cc_start: 0.9304 (p) cc_final: 0.8919 (p) REVERT: AJ 3 TYR cc_start: 0.6794 (m-80) cc_final: 0.6460 (m-80) REVERT: AP 10 SER cc_start: 0.8909 (p) cc_final: 0.8677 (t) REVERT: AS 3 TYR cc_start: 0.6461 (m-80) cc_final: 0.6067 (m-80) REVERT: AV 3 TYR cc_start: 0.7233 (m-80) cc_final: 0.6790 (m-80) REVERT: AW 3 TYR cc_start: 0.6602 (m-80) cc_final: 0.6061 (m-10) REVERT: AZ 3 TYR cc_start: 0.7442 (m-80) cc_final: 0.7000 (m-80) REVERT: A0 3 TYR cc_start: 0.6494 (OUTLIER) cc_final: 0.5891 (m-80) REVERT: A0 10 SER cc_start: 0.9231 (p) cc_final: 0.8886 (p) REVERT: A7 10 SER cc_start: 0.8897 (p) cc_final: 0.8633 (t) REVERT: A8 10 SER cc_start: 0.9048 (p) cc_final: 0.8778 (p) REVERT: BA 3 TYR cc_start: 0.6488 (m-80) cc_final: 0.6148 (m-80) REVERT: BE 3 TYR cc_start: 0.6459 (m-80) cc_final: 0.5970 (m-10) REVERT: BG 3 TYR cc_start: 0.6162 (m-80) cc_final: 0.5843 (m-80) REVERT: BH 3 TYR cc_start: 0.7472 (m-80) cc_final: 0.6997 (m-80) REVERT: BI 10 SER cc_start: 0.9211 (p) cc_final: 0.8973 (p) REVERT: BP 10 SER cc_start: 0.9019 (p) cc_final: 0.8710 (t) REVERT: BQ 10 SER cc_start: 0.9073 (p) cc_final: 0.8811 (p) REVERT: BV 3 TYR cc_start: 0.7000 (m-80) cc_final: 0.6647 (m-80) REVERT: BW 3 TYR cc_start: 0.6361 (m-80) cc_final: 0.5985 (m-80) REVERT: BZ 3 TYR cc_start: 0.7260 (m-80) cc_final: 0.6807 (m-80) REVERT: B0 3 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.6167 (m-80) REVERT: B0 10 SER cc_start: 0.9237 (p) cc_final: 0.8897 (p) REVERT: B1 3 TYR cc_start: 0.6815 (m-80) cc_final: 0.6560 (m-80) REVERT: B7 10 SER cc_start: 0.8834 (p) cc_final: 0.8619 (p) REVERT: CA 3 TYR cc_start: 0.6130 (m-80) cc_final: 0.5463 (t80) REVERT: CB 2 HIS cc_start: 0.5869 (m-70) cc_final: 0.3546 (p-80) REVERT: CI 3 TYR cc_start: 0.7262 (OUTLIER) cc_final: 0.6755 (m-10) REVERT: CI 10 SER cc_start: 0.8960 (p) cc_final: 0.8541 (p) outliers start: 16 outliers final: 10 residues processed: 225 average time/residue: 0.1083 time to fit residues: 35.6931 Evaluate side-chains 203 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 TYR Chi-restraints excluded: chain Q residue 3 TYR Chi-restraints excluded: chain U residue 3 TYR Chi-restraints excluded: chain 8 residue 3 TYR Chi-restraints excluded: chain c residue 3 TYR Chi-restraints excluded: chain q residue 3 TYR Chi-restraints excluded: chain u residue 3 TYR Chi-restraints excluded: chain AI residue 3 TYR Chi-restraints excluded: chain AM residue 3 TYR Chi-restraints excluded: chain A0 residue 3 TYR Chi-restraints excluded: chain A4 residue 3 TYR Chi-restraints excluded: chain BI residue 3 TYR Chi-restraints excluded: chain BM residue 3 TYR Chi-restraints excluded: chain B0 residue 3 TYR Chi-restraints excluded: chain B4 residue 3 TYR Chi-restraints excluded: chain CI residue 3 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 2 HIS 9 2 HIS r 2 HIS AJ 2 HIS A1 2 HIS BJ 2 HIS B1 2 HIS CB 2 HIS CJ 2 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.172745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.108836 restraints weight = 12632.271| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 4.85 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12816 Z= 0.125 Angle : 0.606 6.061 16128 Z= 0.260 Chirality : 0.064 0.142 1584 Planarity : 0.003 0.021 1728 Dihedral : 11.228 59.736 2624 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 1.04 % Allowed : 8.25 % Favored : 90.71 % 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: -4.81 (0.20), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.002 TYRB1 3 HIS 0.004 0.001 HISAJ 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (12528) covalent geometry : angle 0.60606 / 0.26 (16128) Misc. bond : bond 0.00040 / 0.03 ( 288) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 SER cc_start: 0.8384 (p) cc_final: 0.8004 (t) REVERT: G 10 SER cc_start: 0.8930 (p) cc_final: 0.8500 (p) REVERT: M 3 TYR cc_start: 0.5436 (m-80) cc_final: 0.4739 (m-80) REVERT: O 3 TYR cc_start: 0.5767 (m-80) cc_final: 0.5509 (m-80) REVERT: P 3 TYR cc_start: 0.6485 (m-80) cc_final: 0.5975 (m-80) REVERT: Q 3 TYR cc_start: 0.5399 (m-80) cc_final: 0.5162 (m-80) REVERT: Q 10 SER cc_start: 0.8826 (p) cc_final: 0.8168 (p) REVERT: R 3 TYR cc_start: 0.5700 (m-80) cc_final: 0.5342 (m-80) REVERT: V 3 TYR cc_start: 0.7008 (m-80) cc_final: 0.6762 (m-80) REVERT: W 3 TYR cc_start: 0.7666 (m-80) cc_final: 0.7335 (m-80) REVERT: X 11 LYS cc_start: 0.7812 (ttmt) cc_final: 0.6954 (tmtt) REVERT: 0 11 LYS cc_start: 0.7623 (mmtt) cc_final: 0.6286 (ttpt) REVERT: 4 3 TYR cc_start: 0.6369 (m-80) cc_final: 0.5673 (p90) REVERT: 5 5 ILE cc_start: 0.8755 (mt) cc_final: 0.8531 (mp) REVERT: 6 3 TYR cc_start: 0.6406 (m-80) cc_final: 0.5983 (m-80) REVERT: 6 11 LYS cc_start: 0.7356 (mttt) cc_final: 0.5906 (tmtt) REVERT: 7 3 TYR cc_start: 0.7328 (m-80) cc_final: 0.6709 (m-80) REVERT: 8 3 TYR cc_start: 0.5968 (m-80) cc_final: 0.4460 (p90) REVERT: g 10 SER cc_start: 0.8570 (p) cc_final: 0.8092 (p) REVERT: o 3 TYR cc_start: 0.5798 (m-80) cc_final: 0.5578 (m-80) REVERT: p 3 TYR cc_start: 0.6708 (m-80) cc_final: 0.6250 (m-80) REVERT: q 10 SER cc_start: 0.8839 (p) cc_final: 0.8183 (p) REVERT: r 3 TYR cc_start: 0.5640 (m-80) cc_final: 0.4812 (m-80) REVERT: y 10 SER cc_start: 0.8833 (p) cc_final: 0.8284 (p) REVERT: AH 3 TYR cc_start: 0.6556 (m-80) cc_final: 0.6041 (m-80) REVERT: AI 10 SER cc_start: 0.8875 (p) cc_final: 0.8280 (p) REVERT: AJ 3 TYR cc_start: 0.5527 (m-80) cc_final: 0.4764 (m-80) REVERT: AP 10 SER cc_start: 0.8084 (p) cc_final: 0.7818 (t) REVERT: AV 3 TYR cc_start: 0.6283 (m-80) cc_final: 0.5671 (m-80) REVERT: AW 3 TYR cc_start: 0.5521 (m-80) cc_final: 0.5195 (m-80) REVERT: AZ 3 TYR cc_start: 0.6564 (m-80) cc_final: 0.6110 (m-80) REVERT: A0 10 SER cc_start: 0.8866 (p) cc_final: 0.8203 (p) REVERT: A7 10 SER cc_start: 0.8426 (p) cc_final: 0.8135 (p) REVERT: A8 10 SER cc_start: 0.8987 (p) cc_final: 0.8448 (p) REVERT: BE 3 TYR cc_start: 0.5410 (m-80) cc_final: 0.5018 (m-80) REVERT: BH 3 TYR cc_start: 0.6506 (m-80) cc_final: 0.5952 (m-80) REVERT: BI 10 SER cc_start: 0.8898 (p) cc_final: 0.8331 (p) REVERT: BP 10 SER cc_start: 0.8576 (p) cc_final: 0.8338 (p) REVERT: BQ 10 SER cc_start: 0.9138 (p) cc_final: 0.8620 (p) REVERT: BV 3 TYR cc_start: 0.6376 (m-80) cc_final: 0.5709 (m-80) REVERT: BZ 3 TYR cc_start: 0.6406 (m-80) cc_final: 0.5821 (m-80) REVERT: B0 10 SER cc_start: 0.8831 (p) cc_final: 0.8243 (p) REVERT: B1 3 TYR cc_start: 0.5877 (m-80) cc_final: 0.5629 (m-80) REVERT: CI 10 SER cc_start: 0.8391 (p) cc_final: 0.7784 (p) outliers start: 12 outliers final: 10 residues processed: 176 average time/residue: 0.0983 time to fit residues: 25.4850 Evaluate side-chains 170 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain 3 residue 3 TYR Chi-restraints excluded: chain f residue 3 TYR Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain o residue 11 LYS Chi-restraints excluded: chain t residue 10 SER Chi-restraints excluded: chain AD residue 3 TYR Chi-restraints excluded: chain BL residue 10 SER Chi-restraints excluded: chain B9 residue 10 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 130 optimal weight: 0.0040 chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 2 HIS ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 2 HIS ** 6 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 2 HIS g 2 HIS ** o 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 2 HIS ** AG 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AP 2 HIS ** AY 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A7 2 HIS ** BG 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BP 2 HIS B7 2 HIS CB 2 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.171223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.103146 restraints weight = 13507.028| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 5.06 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12816 Z= 0.186 Angle : 0.632 4.910 16128 Z= 0.286 Chirality : 0.065 0.140 1584 Planarity : 0.004 0.027 1728 Dihedral : 11.688 59.956 2592 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.93 % Favored : 85.07 % Rotamer: Outliers : 1.82 % Allowed : 8.59 % Favored : 89.58 % 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: -4.84 (0.20), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.003 TYRBW 3 HIS 0.005 0.000 HIS g 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (12528) covalent geometry : angle 0.63172 / 0.29 (16128) Misc. bond : bond 0.00068 / 0.05 ( 288) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 SER cc_start: 0.8627 (p) cc_final: 0.8383 (p) REVERT: M 3 TYR cc_start: 0.5530 (m-80) cc_final: 0.4810 (m-80) REVERT: O 3 TYR cc_start: 0.5782 (m-80) cc_final: 0.5536 (m-80) REVERT: P 3 TYR cc_start: 0.6525 (m-80) cc_final: 0.6244 (m-80) REVERT: Q 3 TYR cc_start: 0.5508 (m-80) cc_final: 0.4842 (m-10) REVERT: Q 10 SER cc_start: 0.8904 (p) cc_final: 0.8348 (p) REVERT: R 3 TYR cc_start: 0.5899 (m-80) cc_final: 0.5542 (m-80) REVERT: T 10 SER cc_start: 0.7704 (t) cc_final: 0.7019 (m) REVERT: V 3 TYR cc_start: 0.7054 (m-80) cc_final: 0.6762 (m-80) REVERT: W 3 TYR cc_start: 0.7849 (m-80) cc_final: 0.7592 (m-80) REVERT: X 11 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7246 (tmtt) REVERT: 0 11 LYS cc_start: 0.7736 (mmtt) cc_final: 0.6458 (tttm) REVERT: 3 2 HIS cc_start: 0.4316 (m-70) cc_final: 0.4105 (m-70) REVERT: 4 3 TYR cc_start: 0.6268 (m-80) cc_final: 0.5530 (p90) REVERT: 5 5 ILE cc_start: 0.8813 (mt) cc_final: 0.8562 (mp) REVERT: 6 3 TYR cc_start: 0.6610 (m-80) cc_final: 0.6099 (m-80) REVERT: 7 3 TYR cc_start: 0.7285 (m-80) cc_final: 0.6700 (m-80) REVERT: 9 3 TYR cc_start: 0.6415 (m-80) cc_final: 0.6152 (m-80) REVERT: g 10 SER cc_start: 0.8861 (p) cc_final: 0.8363 (p) REVERT: p 3 TYR cc_start: 0.6752 (m-80) cc_final: 0.6373 (m-80) REVERT: q 3 TYR cc_start: 0.5977 (m-80) cc_final: 0.5565 (m-80) REVERT: q 10 SER cc_start: 0.8918 (p) cc_final: 0.8302 (p) REVERT: r 3 TYR cc_start: 0.5637 (m-80) cc_final: 0.5408 (m-80) REVERT: y 10 SER cc_start: 0.9044 (p) cc_final: 0.8523 (p) REVERT: AH 3 TYR cc_start: 0.6580 (m-80) cc_final: 0.6170 (m-80) REVERT: AI 10 SER cc_start: 0.9010 (p) cc_final: 0.8445 (p) REVERT: AJ 3 TYR cc_start: 0.5909 (m-80) cc_final: 0.5606 (m-80) REVERT: AP 10 SER cc_start: 0.8707 (p) cc_final: 0.8148 (t) REVERT: AV 3 TYR cc_start: 0.6169 (m-80) cc_final: 0.5725 (m-80) REVERT: AW 3 TYR cc_start: 0.5607 (m-80) cc_final: 0.5370 (m-80) REVERT: AZ 3 TYR cc_start: 0.6622 (m-80) cc_final: 0.6278 (m-80) REVERT: A0 10 SER cc_start: 0.9032 (p) cc_final: 0.8498 (p) REVERT: A7 10 SER cc_start: 0.8618 (p) cc_final: 0.8380 (p) REVERT: A8 10 SER cc_start: 0.9206 (p) cc_final: 0.8669 (p) REVERT: BD 3 TYR cc_start: 0.6621 (m-80) cc_final: 0.6004 (m-80) REVERT: BE 3 TYR cc_start: 0.5425 (m-80) cc_final: 0.4904 (m-80) REVERT: BG 3 TYR cc_start: 0.5765 (m-80) cc_final: 0.5521 (m-80) REVERT: BH 3 TYR cc_start: 0.6358 (m-80) cc_final: 0.5911 (m-80) REVERT: BI 10 SER cc_start: 0.8958 (p) cc_final: 0.8406 (p) REVERT: BQ 10 SER cc_start: 0.9184 (p) cc_final: 0.8755 (p) REVERT: BV 3 TYR cc_start: 0.6299 (m-80) cc_final: 0.6072 (m-80) REVERT: BZ 3 TYR cc_start: 0.6515 (m-80) cc_final: 0.6058 (m-80) REVERT: B0 10 SER cc_start: 0.8974 (p) cc_final: 0.8454 (p) REVERT: B1 3 TYR cc_start: 0.5940 (m-80) cc_final: 0.5698 (m-80) REVERT: B1 10 SER cc_start: 0.8605 (p) cc_final: 0.8344 (p) REVERT: CE 3 TYR cc_start: 0.5820 (OUTLIER) cc_final: 0.4655 (m-80) REVERT: CI 10 SER cc_start: 0.8448 (p) cc_final: 0.7994 (p) outliers start: 21 outliers final: 19 residues processed: 194 average time/residue: 0.0927 time to fit residues: 27.9298 Evaluate side-chains 187 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain 3 residue 3 TYR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain f residue 3 TYR Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain o residue 11 LYS Chi-restraints excluded: chain w residue 10 SER Chi-restraints excluded: chain AM residue 3 TYR Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AQ residue 10 SER Chi-restraints excluded: chain A6 residue 10 SER Chi-restraints excluded: chain BH residue 10 SER Chi-restraints excluded: chain BZ residue 10 SER Chi-restraints excluded: chain B9 residue 10 SER Chi-restraints excluded: chain CE residue 3 TYR Chi-restraints excluded: chain CH residue 10 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 117 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 102 optimal weight: 0.0770 chunk 103 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** y 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 2 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.170780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.100468 restraints weight = 14465.583| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 5.26 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12816 Z= 0.201 Angle : 0.616 5.015 16128 Z= 0.280 Chirality : 0.066 0.141 1584 Planarity : 0.004 0.027 1728 Dihedral : 11.722 59.872 2592 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.80 % Favored : 86.20 % Rotamer: Outliers : 2.95 % Allowed : 10.59 % Favored : 86.46 % 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: -4.76 (0.20), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.002 TYR g 3 HIS 0.005 0.000 HIS G 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.20 (12528) covalent geometry : angle 0.61601 / 0.28 (16128) Misc. bond : bond 0.00068 / 0.04 ( 288) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 SER cc_start: 0.8590 (p) cc_final: 0.8335 (p) REVERT: H 3 TYR cc_start: 0.5375 (m-80) cc_final: 0.4409 (m-80) REVERT: K 10 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8122 (t) REVERT: M 3 TYR cc_start: 0.5721 (m-80) cc_final: 0.4937 (m-80) REVERT: O 3 TYR cc_start: 0.5690 (m-80) cc_final: 0.5486 (m-80) REVERT: P 3 TYR cc_start: 0.6434 (m-80) cc_final: 0.6218 (m-80) REVERT: Q 3 TYR cc_start: 0.5527 (m-80) cc_final: 0.5029 (m-80) REVERT: Q 10 SER cc_start: 0.8805 (p) cc_final: 0.8247 (p) REVERT: R 3 TYR cc_start: 0.6034 (m-80) cc_final: 0.5655 (m-80) REVERT: R 10 SER cc_start: 0.8734 (p) cc_final: 0.8519 (p) REVERT: T 10 SER cc_start: 0.7962 (t) cc_final: 0.7303 (m) REVERT: V 3 TYR cc_start: 0.7107 (m-80) cc_final: 0.6898 (m-80) REVERT: W 3 TYR cc_start: 0.7775 (m-80) cc_final: 0.7547 (m-80) REVERT: X 11 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7334 (tmtt) REVERT: 0 11 LYS cc_start: 0.7861 (mmtt) cc_final: 0.6695 (ttpt) REVERT: 2 3 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.5445 (p90) REVERT: 3 2 HIS cc_start: 0.4191 (m-70) cc_final: 0.3932 (m90) REVERT: 4 3 TYR cc_start: 0.6376 (m-80) cc_final: 0.5892 (p90) REVERT: 5 5 ILE cc_start: 0.8816 (mt) cc_final: 0.8566 (mp) REVERT: 6 3 TYR cc_start: 0.6682 (m-80) cc_final: 0.6095 (m-80) REVERT: 7 3 TYR cc_start: 0.7285 (m-80) cc_final: 0.6753 (m-80) REVERT: g 10 SER cc_start: 0.8856 (p) cc_final: 0.8421 (p) REVERT: h 3 TYR cc_start: 0.5745 (m-80) cc_final: 0.5391 (m-80) REVERT: m 3 TYR cc_start: 0.5964 (m-80) cc_final: 0.5362 (m-80) REVERT: p 3 TYR cc_start: 0.6772 (m-80) cc_final: 0.6396 (m-80) REVERT: q 10 SER cc_start: 0.8782 (p) cc_final: 0.8196 (p) REVERT: x 3 TYR cc_start: 0.6322 (m-80) cc_final: 0.5856 (m-80) REVERT: z 3 TYR cc_start: 0.5560 (m-80) cc_final: 0.4639 (m-80) REVERT: AE 3 TYR cc_start: 0.5790 (m-80) cc_final: 0.5549 (m-80) REVERT: AH 3 TYR cc_start: 0.6601 (m-80) cc_final: 0.6272 (m-80) REVERT: AI 10 SER cc_start: 0.8876 (p) cc_final: 0.8350 (p) REVERT: AJ 3 TYR cc_start: 0.5899 (m-80) cc_final: 0.5601 (m-80) REVERT: AP 10 SER cc_start: 0.8719 (p) cc_final: 0.8244 (t) REVERT: AR 3 TYR cc_start: 0.5678 (m-80) cc_final: 0.4794 (m-80) REVERT: AV 3 TYR cc_start: 0.6212 (m-80) cc_final: 0.5552 (m-80) REVERT: AW 3 TYR cc_start: 0.5719 (m-80) cc_final: 0.5328 (m-10) REVERT: AZ 3 TYR cc_start: 0.6536 (m-80) cc_final: 0.6223 (m-80) REVERT: A0 10 SER cc_start: 0.8892 (p) cc_final: 0.8454 (p) REVERT: A7 10 SER cc_start: 0.8690 (p) cc_final: 0.8464 (p) REVERT: A8 10 SER cc_start: 0.9190 (p) cc_final: 0.8731 (p) REVERT: A9 3 TYR cc_start: 0.5596 (m-80) cc_final: 0.4773 (m-80) REVERT: BD 3 TYR cc_start: 0.6628 (m-80) cc_final: 0.6060 (m-80) REVERT: BH 3 TYR cc_start: 0.6465 (m-80) cc_final: 0.6090 (m-80) REVERT: BI 10 SER cc_start: 0.8890 (p) cc_final: 0.8372 (p) REVERT: BK 10 SER cc_start: 0.8803 (p) cc_final: 0.8171 (p) REVERT: BR 3 TYR cc_start: 0.5250 (m-80) cc_final: 0.4615 (m-80) REVERT: BV 3 TYR cc_start: 0.6085 (m-80) cc_final: 0.5748 (m-80) REVERT: BZ 3 TYR cc_start: 0.6512 (m-80) cc_final: 0.5161 (m-80) REVERT: B0 10 SER cc_start: 0.8773 (p) cc_final: 0.8312 (p) REVERT: B1 3 TYR cc_start: 0.6069 (m-80) cc_final: 0.5848 (m-80) REVERT: B1 10 SER cc_start: 0.8609 (p) cc_final: 0.8386 (p) REVERT: CE 3 TYR cc_start: 0.6040 (OUTLIER) cc_final: 0.4556 (m-80) REVERT: CH 3 TYR cc_start: 0.7034 (m-80) cc_final: 0.6490 (m-80) REVERT: CI 10 SER cc_start: 0.8713 (p) cc_final: 0.8383 (p) outliers start: 34 outliers final: 29 residues processed: 200 average time/residue: 0.0854 time to fit residues: 26.4022 Evaluate side-chains 207 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain X residue 3 TYR Chi-restraints excluded: chain 2 residue 3 TYR Chi-restraints excluded: chain 3 residue 3 TYR Chi-restraints excluded: chain 7 residue 10 SER Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain f residue 3 TYR Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain o residue 11 LYS Chi-restraints excluded: chain w residue 10 SER Chi-restraints excluded: chain AD residue 3 TYR Chi-restraints excluded: chain AH residue 10 SER Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AQ residue 10 SER Chi-restraints excluded: chain AU residue 10 SER Chi-restraints excluded: chain AZ residue 10 SER Chi-restraints excluded: chain A6 residue 10 SER Chi-restraints excluded: chain BH residue 10 SER Chi-restraints excluded: chain BO residue 10 SER Chi-restraints excluded: chain BZ residue 10 SER Chi-restraints excluded: chain B4 residue 10 SER Chi-restraints excluded: chain B6 residue 10 SER Chi-restraints excluded: chain B9 residue 10 SER Chi-restraints excluded: chain CE residue 3 TYR Chi-restraints excluded: chain CH residue 10 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 2 HIS ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 2 HIS ** o 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 2 HIS ** AY 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.172251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.100295 restraints weight = 15020.025| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 5.32 r_work: 0.3680 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12816 Z= 0.261 Angle : 0.669 4.430 16128 Z= 0.313 Chirality : 0.069 0.156 1584 Planarity : 0.005 0.040 1728 Dihedral : 12.407 59.127 2592 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.83 % Favored : 79.17 % Rotamer: Outliers : 4.25 % Allowed : 11.20 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.20), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.030 0.003 TYRAI 3 HIS 0.005 0.001 HISAQ 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.26 (12528) covalent geometry : angle 0.66945 / 0.31 (16128) Misc. bond : bond 0.00084 / 0.06 ( 288) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 SER cc_start: 0.8745 (p) cc_final: 0.8459 (p) REVERT: L 3 TYR cc_start: 0.6307 (m-80) cc_final: 0.5921 (m-80) REVERT: M 3 TYR cc_start: 0.5855 (m-80) cc_final: 0.4971 (m-80) REVERT: Q 10 SER cc_start: 0.8877 (p) cc_final: 0.8272 (p) REVERT: R 3 TYR cc_start: 0.6335 (m-80) cc_final: 0.5955 (m-80) REVERT: T 10 SER cc_start: 0.7823 (t) cc_final: 0.7247 (m) REVERT: X 11 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7461 (tmtt) REVERT: Z 3 TYR cc_start: 0.6404 (m-80) cc_final: 0.5664 (p90) REVERT: 0 11 LYS cc_start: 0.7819 (mmtt) cc_final: 0.6611 (tttm) REVERT: 1 3 TYR cc_start: 0.6937 (OUTLIER) cc_final: 0.5638 (p90) REVERT: 2 3 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.5469 (p90) REVERT: 3 2 HIS cc_start: 0.4205 (m-70) cc_final: 0.3820 (m90) REVERT: 4 3 TYR cc_start: 0.6673 (m-80) cc_final: 0.6163 (p90) REVERT: 5 5 ILE cc_start: 0.8854 (mt) cc_final: 0.8630 (mp) REVERT: 6 3 TYR cc_start: 0.6897 (m-80) cc_final: 0.6267 (m-80) REVERT: 7 3 TYR cc_start: 0.7747 (m-80) cc_final: 0.7248 (m-80) REVERT: g 10 SER cc_start: 0.8920 (p) cc_final: 0.8432 (p) REVERT: h 3 TYR cc_start: 0.6403 (m-80) cc_final: 0.6140 (m-80) REVERT: m 3 TYR cc_start: 0.6342 (m-80) cc_final: 0.5488 (m-80) REVERT: p 3 TYR cc_start: 0.7105 (m-80) cc_final: 0.6767 (m-80) REVERT: q 10 SER cc_start: 0.8859 (p) cc_final: 0.8242 (p) REVERT: r 3 TYR cc_start: 0.6038 (m-80) cc_final: 0.5537 (m-80) REVERT: AE 3 TYR cc_start: 0.6100 (m-80) cc_final: 0.5448 (m-80) REVERT: AH 3 TYR cc_start: 0.7089 (m-80) cc_final: 0.6848 (m-80) REVERT: AI 10 SER cc_start: 0.8920 (p) cc_final: 0.8372 (p) REVERT: AJ 3 TYR cc_start: 0.6296 (m-80) cc_final: 0.5906 (m-80) REVERT: AP 10 SER cc_start: 0.8910 (p) cc_final: 0.8288 (t) REVERT: AW 3 TYR cc_start: 0.6105 (m-80) cc_final: 0.5395 (m-10) REVERT: A0 10 SER cc_start: 0.9018 (p) cc_final: 0.8502 (p) REVERT: A7 10 SER cc_start: 0.8836 (p) cc_final: 0.8564 (p) REVERT: A8 10 SER cc_start: 0.9222 (p) cc_final: 0.8628 (p) REVERT: BD 3 TYR cc_start: 0.6542 (m-80) cc_final: 0.6162 (m-80) REVERT: BE 3 TYR cc_start: 0.6037 (m-80) cc_final: 0.5797 (m-80) REVERT: BH 3 TYR cc_start: 0.6767 (m-80) cc_final: 0.6504 (m-80) REVERT: BI 10 SER cc_start: 0.8851 (p) cc_final: 0.8312 (p) REVERT: BK 10 SER cc_start: 0.9039 (p) cc_final: 0.8426 (p) REVERT: BU 3 TYR cc_start: 0.6855 (m-80) cc_final: 0.6639 (m-80) REVERT: BV 3 TYR cc_start: 0.6231 (m-80) cc_final: 0.5983 (m-80) REVERT: BZ 3 TYR cc_start: 0.6865 (m-80) cc_final: 0.5766 (m-80) REVERT: B0 10 SER cc_start: 0.8955 (p) cc_final: 0.8414 (p) REVERT: B1 3 TYR cc_start: 0.6454 (m-80) cc_final: 0.6242 (m-80) REVERT: CA 3 TYR cc_start: 0.5897 (m-80) cc_final: 0.5288 (m-80) REVERT: CB 3 TYR cc_start: 0.6600 (m-80) cc_final: 0.6236 (m-80) REVERT: CC 3 TYR cc_start: 0.6175 (m-80) cc_final: 0.5266 (m-80) REVERT: CE 3 TYR cc_start: 0.5904 (OUTLIER) cc_final: 0.4510 (m-80) REVERT: CH 3 TYR cc_start: 0.7317 (m-80) cc_final: 0.6713 (m-80) REVERT: CI 3 TYR cc_start: 0.6619 (m-80) cc_final: 0.6337 (m-80) REVERT: CI 10 SER cc_start: 0.8594 (p) cc_final: 0.8155 (p) outliers start: 49 outliers final: 42 residues processed: 205 average time/residue: 0.0958 time to fit residues: 29.9656 Evaluate side-chains 228 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 TYR 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 H residue 10 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain X residue 3 TYR Chi-restraints excluded: chain 1 residue 3 TYR Chi-restraints excluded: chain 2 residue 3 TYR Chi-restraints excluded: chain 3 residue 3 TYR Chi-restraints excluded: chain 7 residue 10 SER Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain f residue 3 TYR Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain o residue 11 LYS Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain s residue 10 SER Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain w residue 10 SER Chi-restraints excluded: chain AC residue 10 SER Chi-restraints excluded: chain AD residue 3 TYR Chi-restraints excluded: chain AH residue 10 SER Chi-restraints excluded: chain AK residue 10 SER Chi-restraints excluded: chain AN residue 10 SER Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AP residue 3 TYR Chi-restraints excluded: chain AQ residue 10 SER Chi-restraints excluded: chain AU residue 10 SER Chi-restraints excluded: chain AZ residue 10 SER Chi-restraints excluded: chain A6 residue 10 SER Chi-restraints excluded: chain BH residue 10 SER Chi-restraints excluded: chain BO residue 10 SER Chi-restraints excluded: chain BZ residue 10 SER Chi-restraints excluded: chain B2 residue 10 SER Chi-restraints excluded: chain B6 residue 10 SER Chi-restraints excluded: chain B7 residue 3 TYR Chi-restraints excluded: chain B9 residue 10 SER Chi-restraints excluded: chain CE residue 3 TYR Chi-restraints excluded: chain CH residue 10 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 2 HIS ** 6 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 2 HIS ** CB 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 2 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.171478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.097147 restraints weight = 18084.152| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 5.68 r_work: 0.3649 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 12816 Z= 0.275 Angle : 0.676 4.650 16128 Z= 0.320 Chirality : 0.070 0.173 1584 Planarity : 0.006 0.041 1728 Dihedral : 12.311 59.507 2592 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.23 % Favored : 79.77 % Rotamer: Outliers : 4.95 % Allowed : 10.85 % Favored : 84.20 % 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: -4.90 (0.20), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.031 0.003 TYR g 3 HIS 0.005 0.001 HISAQ 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.28 (12528) covalent geometry : angle 0.67637 / 0.32 (16128) Misc. bond : bond 0.00088 / 0.06 ( 288) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 SER cc_start: 0.8793 (p) cc_final: 0.8506 (p) REVERT: L 3 TYR cc_start: 0.6261 (m-80) cc_final: 0.6037 (m-80) REVERT: M 3 TYR cc_start: 0.5926 (m-80) cc_final: 0.4986 (m-80) REVERT: Q 10 SER cc_start: 0.8825 (p) cc_final: 0.8241 (p) REVERT: R 3 TYR cc_start: 0.6357 (m-80) cc_final: 0.5972 (m-80) REVERT: T 10 SER cc_start: 0.8091 (t) cc_final: 0.7504 (m) REVERT: Y 3 TYR cc_start: 0.6438 (OUTLIER) cc_final: 0.5482 (p90) REVERT: Z 3 TYR cc_start: 0.6533 (m-80) cc_final: 0.5778 (p90) REVERT: 0 11 LYS cc_start: 0.7788 (mmtt) cc_final: 0.6403 (tttm) REVERT: 1 3 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.5285 (p90) REVERT: 2 3 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.5569 (p90) REVERT: 3 2 HIS cc_start: 0.4081 (m-70) cc_final: 0.3754 (m90) REVERT: 4 3 TYR cc_start: 0.6670 (m-80) cc_final: 0.6153 (p90) REVERT: 5 5 ILE cc_start: 0.8827 (mt) cc_final: 0.8606 (mp) REVERT: 6 3 TYR cc_start: 0.6918 (m-80) cc_final: 0.6311 (m-80) REVERT: 7 3 TYR cc_start: 0.7775 (m-80) cc_final: 0.7284 (m-80) REVERT: 9 3 TYR cc_start: 0.7130 (m-80) cc_final: 0.6736 (m-80) REVERT: g 10 SER cc_start: 0.8957 (p) cc_final: 0.8533 (p) REVERT: k 3 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.5411 (m-80) REVERT: l 2 HIS cc_start: 0.4043 (m90) cc_final: 0.3750 (m-70) REVERT: m 3 TYR cc_start: 0.6400 (m-80) cc_final: 0.5779 (m-80) REVERT: q 10 SER cc_start: 0.8840 (p) cc_final: 0.8221 (p) REVERT: r 3 TYR cc_start: 0.6238 (m-80) cc_final: 0.5855 (m-80) REVERT: AE 3 TYR cc_start: 0.6152 (m-80) cc_final: 0.5879 (m-80) REVERT: AI 10 SER cc_start: 0.8775 (p) cc_final: 0.8223 (p) REVERT: AJ 3 TYR cc_start: 0.6424 (m-80) cc_final: 0.6029 (m-80) REVERT: AP 10 SER cc_start: 0.8837 (p) cc_final: 0.8218 (t) REVERT: AW 3 TYR cc_start: 0.6350 (m-80) cc_final: 0.5832 (m-10) REVERT: A0 10 SER cc_start: 0.8981 (p) cc_final: 0.8506 (p) REVERT: A2 10 SER cc_start: 0.9017 (p) cc_final: 0.8420 (p) REVERT: A7 10 SER cc_start: 0.8862 (p) cc_final: 0.8598 (p) REVERT: BD 3 TYR cc_start: 0.6523 (m-80) cc_final: 0.6087 (m-80) REVERT: BE 3 TYR cc_start: 0.6090 (m-80) cc_final: 0.5792 (m-80) REVERT: BI 10 SER cc_start: 0.8821 (p) cc_final: 0.8308 (p) REVERT: BK 10 SER cc_start: 0.8841 (p) cc_final: 0.8253 (p) REVERT: BT 3 TYR cc_start: 0.6386 (m-80) cc_final: 0.5982 (m-80) REVERT: BU 3 TYR cc_start: 0.6833 (m-80) cc_final: 0.6565 (m-80) REVERT: BV 3 TYR cc_start: 0.6216 (m-80) cc_final: 0.5996 (m-80) REVERT: BZ 3 TYR cc_start: 0.6864 (m-80) cc_final: 0.5845 (m-80) REVERT: B0 10 SER cc_start: 0.8850 (p) cc_final: 0.8313 (p) REVERT: B8 3 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.4769 (m-80) REVERT: CA 3 TYR cc_start: 0.5918 (m-80) cc_final: 0.5300 (m-80) REVERT: CC 3 TYR cc_start: 0.6410 (m-80) cc_final: 0.5394 (m-80) REVERT: CD 11 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7902 (mtmm) REVERT: CE 3 TYR cc_start: 0.5902 (OUTLIER) cc_final: 0.4544 (m-10) REVERT: CH 3 TYR cc_start: 0.7380 (m-80) cc_final: 0.6788 (m-80) REVERT: CI 3 TYR cc_start: 0.6691 (m-80) cc_final: 0.6343 (m-80) REVERT: CI 10 SER cc_start: 0.8598 (p) cc_final: 0.8183 (p) outliers start: 57 outliers final: 45 residues processed: 211 average time/residue: 0.0969 time to fit residues: 31.1840 Evaluate side-chains 228 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain X residue 3 TYR Chi-restraints excluded: chain Y residue 3 TYR Chi-restraints excluded: chain 1 residue 3 TYR Chi-restraints excluded: chain 2 residue 3 TYR Chi-restraints excluded: chain 3 residue 3 TYR Chi-restraints excluded: chain 7 residue 10 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain f residue 3 TYR Chi-restraints excluded: chain k residue 3 TYR Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain o residue 11 LYS Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain s residue 10 SER Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain w residue 10 SER Chi-restraints excluded: chain AC residue 10 SER Chi-restraints excluded: chain AD residue 3 TYR Chi-restraints excluded: chain AH residue 10 SER Chi-restraints excluded: chain AK residue 10 SER Chi-restraints excluded: chain AN residue 10 SER Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AP residue 3 TYR Chi-restraints excluded: chain AQ residue 3 TYR Chi-restraints excluded: chain AQ residue 10 SER Chi-restraints excluded: chain AU residue 10 SER Chi-restraints excluded: chain AZ residue 10 SER Chi-restraints excluded: chain A4 residue 10 SER Chi-restraints excluded: chain A6 residue 10 SER Chi-restraints excluded: chain A7 residue 3 TYR Chi-restraints excluded: chain A8 residue 3 TYR Chi-restraints excluded: chain BH residue 10 SER Chi-restraints excluded: chain BO residue 10 SER Chi-restraints excluded: chain BP residue 3 TYR Chi-restraints excluded: chain BZ residue 10 SER Chi-restraints excluded: chain B2 residue 10 SER Chi-restraints excluded: chain B4 residue 10 SER Chi-restraints excluded: chain B6 residue 10 SER Chi-restraints excluded: chain B7 residue 3 TYR Chi-restraints excluded: chain B8 residue 3 TYR Chi-restraints excluded: chain B9 residue 10 SER Chi-restraints excluded: chain CD residue 11 LYS Chi-restraints excluded: chain CE residue 3 TYR Chi-restraints excluded: chain CH residue 10 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 87 optimal weight: 0.1980 chunk 143 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 6 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 2 HIS AQ 2 HIS ** CB 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 = 0.4655 r_free = 0.4655 target = 0.174824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.100287 restraints weight = 17081.362| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 5.61 r_work: 0.3703 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12816 Z= 0.148 Angle : 0.547 3.931 16128 Z= 0.250 Chirality : 0.064 0.134 1584 Planarity : 0.005 0.042 1728 Dihedral : 11.217 59.670 2592 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.23 % Favored : 83.77 % Rotamer: Outliers : 3.47 % Allowed : 12.50 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.62 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.029 0.002 TYRAT 3 HIS 0.006 0.000 HIS G 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (12528) covalent geometry : angle 0.54671 / 0.25 (16128) Misc. bond : bond 0.00047 / 0.03 ( 288) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 SER cc_start: 0.8686 (p) cc_final: 0.8143 (p) REVERT: M 3 TYR cc_start: 0.5862 (m-80) cc_final: 0.4995 (m-80) REVERT: Q 3 TYR cc_start: 0.5485 (m-80) cc_final: 0.4942 (m-80) REVERT: Q 10 SER cc_start: 0.8775 (p) cc_final: 0.8230 (p) REVERT: T 10 SER cc_start: 0.8024 (t) cc_final: 0.7445 (m) REVERT: Y 3 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.4940 (p90) REVERT: Z 3 TYR cc_start: 0.6478 (m-80) cc_final: 0.5560 (p90) REVERT: 0 11 LYS cc_start: 0.7828 (mmtt) cc_final: 0.6354 (ttpt) REVERT: 1 3 TYR cc_start: 0.5590 (OUTLIER) cc_final: 0.3982 (p90) REVERT: 2 3 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.5352 (p90) REVERT: 3 2 HIS cc_start: 0.4010 (m-70) cc_final: 0.3667 (m90) REVERT: 4 3 TYR cc_start: 0.6540 (m-80) cc_final: 0.5755 (p90) REVERT: 5 5 ILE cc_start: 0.8803 (mt) cc_final: 0.8586 (mp) REVERT: 6 3 TYR cc_start: 0.6819 (m-80) cc_final: 0.6183 (m-80) REVERT: 7 3 TYR cc_start: 0.7742 (m-80) cc_final: 0.7295 (m-80) REVERT: 9 3 TYR cc_start: 0.7144 (m-80) cc_final: 0.6780 (m-80) REVERT: g 10 SER cc_start: 0.8910 (p) cc_final: 0.8531 (p) REVERT: h 3 TYR cc_start: 0.6460 (m-80) cc_final: 0.6230 (m-80) REVERT: l 2 HIS cc_start: 0.4040 (m90) cc_final: 0.3798 (m-70) REVERT: m 3 TYR cc_start: 0.6306 (m-80) cc_final: 0.5415 (m-80) REVERT: q 10 SER cc_start: 0.8806 (p) cc_final: 0.8266 (p) REVERT: r 3 TYR cc_start: 0.6033 (m-80) cc_final: 0.5676 (m-80) REVERT: AE 3 TYR cc_start: 0.6056 (m-80) cc_final: 0.5384 (m-80) REVERT: AI 10 SER cc_start: 0.8806 (p) cc_final: 0.8276 (p) REVERT: AJ 3 TYR cc_start: 0.6351 (m-80) cc_final: 0.5994 (m-80) REVERT: AP 10 SER cc_start: 0.8734 (p) cc_final: 0.8160 (t) REVERT: AW 3 TYR cc_start: 0.6168 (m-80) cc_final: 0.5462 (m-10) REVERT: A0 10 SER cc_start: 0.8882 (p) cc_final: 0.8429 (p) REVERT: A2 10 SER cc_start: 0.8896 (p) cc_final: 0.8321 (p) REVERT: A7 10 SER cc_start: 0.8808 (p) cc_final: 0.8008 (t) REVERT: BD 3 TYR cc_start: 0.6477 (m-80) cc_final: 0.5973 (m-80) REVERT: BE 3 TYR cc_start: 0.5925 (m-80) cc_final: 0.5700 (m-80) REVERT: BI 10 SER cc_start: 0.8776 (p) cc_final: 0.8240 (p) REVERT: BK 10 SER cc_start: 0.8894 (p) cc_final: 0.8393 (p) REVERT: BT 2 HIS cc_start: 0.4011 (m170) cc_final: 0.3680 (m-70) REVERT: BT 3 TYR cc_start: 0.6094 (m-80) cc_final: 0.5336 (m-80) REVERT: BU 3 TYR cc_start: 0.6659 (m-80) cc_final: 0.6268 (m-80) REVERT: BZ 3 TYR cc_start: 0.6773 (m-80) cc_final: 0.5901 (m-80) REVERT: B0 10 SER cc_start: 0.8824 (p) cc_final: 0.8277 (p) REVERT: CB 3 TYR cc_start: 0.7000 (m-80) cc_final: 0.6726 (m-80) REVERT: CC 3 TYR cc_start: 0.6299 (m-80) cc_final: 0.5327 (m-80) REVERT: CD 11 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7787 (mtmm) REVERT: CH 3 TYR cc_start: 0.7299 (m-80) cc_final: 0.7011 (m-80) REVERT: CI 3 TYR cc_start: 0.6691 (m-80) cc_final: 0.6343 (m-80) REVERT: CI 10 SER cc_start: 0.8641 (p) cc_final: 0.8246 (p) outliers start: 40 outliers final: 35 residues processed: 194 average time/residue: 0.1010 time to fit residues: 30.5434 Evaluate side-chains 208 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain X residue 3 TYR Chi-restraints excluded: chain Y residue 3 TYR Chi-restraints excluded: chain 1 residue 3 TYR Chi-restraints excluded: chain 2 residue 3 TYR Chi-restraints excluded: chain 3 residue 3 TYR Chi-restraints excluded: chain 7 residue 10 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain f residue 3 TYR Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain o residue 11 LYS Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain w residue 10 SER Chi-restraints excluded: chain AC residue 10 SER Chi-restraints excluded: chain AD residue 3 TYR Chi-restraints excluded: chain AH residue 10 SER Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AQ residue 10 SER Chi-restraints excluded: chain AU residue 10 SER Chi-restraints excluded: chain AZ residue 10 SER Chi-restraints excluded: chain A4 residue 10 SER Chi-restraints excluded: chain A6 residue 10 SER Chi-restraints excluded: chain BH residue 10 SER Chi-restraints excluded: chain BO residue 10 SER Chi-restraints excluded: chain BQ residue 10 SER Chi-restraints excluded: chain BZ residue 10 SER Chi-restraints excluded: chain B6 residue 10 SER Chi-restraints excluded: chain B9 residue 10 SER Chi-restraints excluded: chain CD residue 11 LYS Chi-restraints excluded: chain CE residue 3 TYR Chi-restraints excluded: chain CH residue 10 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 118 optimal weight: 0.3980 chunk 6 optimal weight: 0.1980 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AQ 2 HIS ** CB 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.175792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.109071 restraints weight = 15814.868| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 5.17 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12816 Z= 0.106 Angle : 0.508 4.088 16128 Z= 0.230 Chirality : 0.062 0.133 1584 Planarity : 0.005 0.040 1728 Dihedral : 10.141 59.409 2592 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 3.30 % Allowed : 12.59 % Favored : 84.11 % 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: -4.43 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.002 TYRA0 3 HIS 0.006 0.000 HIS G 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 (12528) covalent geometry : angle 0.50837 / 0.23 (16128) Misc. bond : bond 0.00030 / 0.02 ( 288) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 TYR cc_start: 0.5776 (m-80) cc_final: 0.4925 (m-80) REVERT: Q 3 TYR cc_start: 0.5639 (m-80) cc_final: 0.5069 (m-80) REVERT: Q 10 SER cc_start: 0.8864 (p) cc_final: 0.8465 (p) REVERT: R 3 TYR cc_start: 0.6060 (m-80) cc_final: 0.5449 (m-80) REVERT: T 10 SER cc_start: 0.8132 (t) cc_final: 0.7534 (m) REVERT: Y 3 TYR cc_start: 0.6188 (OUTLIER) cc_final: 0.4929 (p90) REVERT: Z 3 TYR cc_start: 0.6362 (m-80) cc_final: 0.5630 (p90) REVERT: 0 11 LYS cc_start: 0.8028 (mmtt) cc_final: 0.6434 (ttpt) REVERT: 3 2 HIS cc_start: 0.3808 (m-70) cc_final: 0.3566 (m90) REVERT: 4 3 TYR cc_start: 0.6356 (m-80) cc_final: 0.5743 (p90) REVERT: 5 5 ILE cc_start: 0.8805 (mt) cc_final: 0.8584 (mp) REVERT: 6 3 TYR cc_start: 0.6728 (m-80) cc_final: 0.6019 (m-80) REVERT: 7 3 TYR cc_start: 0.7348 (m-80) cc_final: 0.6913 (m-80) REVERT: 9 3 TYR cc_start: 0.6785 (m-80) cc_final: 0.6407 (m-80) REVERT: g 10 SER cc_start: 0.8885 (p) cc_final: 0.8575 (p) REVERT: l 2 HIS cc_start: 0.4259 (m90) cc_final: 0.3978 (m-70) REVERT: m 3 TYR cc_start: 0.6153 (m-80) cc_final: 0.5326 (m-80) REVERT: p 3 TYR cc_start: 0.6891 (m-80) cc_final: 0.6599 (m-80) REVERT: q 10 SER cc_start: 0.8852 (p) cc_final: 0.8365 (p) REVERT: AE 3 TYR cc_start: 0.6069 (m-80) cc_final: 0.5463 (m-80) REVERT: AI 10 SER cc_start: 0.8893 (p) cc_final: 0.8447 (p) REVERT: AP 10 SER cc_start: 0.8524 (p) cc_final: 0.8104 (t) REVERT: AW 3 TYR cc_start: 0.6062 (m-80) cc_final: 0.5453 (m-10) REVERT: A0 10 SER cc_start: 0.8848 (p) cc_final: 0.8468 (p) REVERT: A1 3 TYR cc_start: 0.5935 (m-80) cc_final: 0.5472 (m-80) REVERT: A7 10 SER cc_start: 0.8701 (p) cc_final: 0.8079 (t) REVERT: BD 3 TYR cc_start: 0.6490 (m-80) cc_final: 0.5980 (m-80) REVERT: BI 10 SER cc_start: 0.8851 (p) cc_final: 0.8411 (p) REVERT: BK 10 SER cc_start: 0.8721 (p) cc_final: 0.8303 (p) REVERT: BT 3 TYR cc_start: 0.6174 (m-80) cc_final: 0.5604 (m-80) REVERT: BZ 3 TYR cc_start: 0.6548 (m-80) cc_final: 0.5495 (m-80) REVERT: B0 10 SER cc_start: 0.8826 (p) cc_final: 0.8350 (p) REVERT: B1 3 TYR cc_start: 0.6302 (m-80) cc_final: 0.5782 (m-80) REVERT: B4 3 TYR cc_start: 0.6842 (m-80) cc_final: 0.5967 (m-80) REVERT: CC 3 TYR cc_start: 0.6195 (m-80) cc_final: 0.5457 (m-80) REVERT: CD 11 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8028 (mtmm) REVERT: CI 3 TYR cc_start: 0.6793 (m-80) cc_final: 0.6428 (m-80) REVERT: CI 10 SER cc_start: 0.8874 (p) cc_final: 0.8492 (p) outliers start: 38 outliers final: 35 residues processed: 190 average time/residue: 0.1039 time to fit residues: 29.8656 Evaluate side-chains 206 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain X residue 3 TYR Chi-restraints excluded: chain Y residue 3 TYR Chi-restraints excluded: chain 3 residue 3 TYR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain o residue 11 LYS Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain w residue 10 SER Chi-restraints excluded: chain AC residue 10 SER Chi-restraints excluded: chain AD residue 3 TYR Chi-restraints excluded: chain AH residue 10 SER Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AQ residue 2 HIS Chi-restraints excluded: chain AQ residue 10 SER Chi-restraints excluded: chain AU residue 10 SER Chi-restraints excluded: chain AZ residue 10 SER Chi-restraints excluded: chain A4 residue 10 SER Chi-restraints excluded: chain A6 residue 10 SER Chi-restraints excluded: chain BH residue 10 SER Chi-restraints excluded: chain BO residue 10 SER Chi-restraints excluded: chain BQ residue 10 SER Chi-restraints excluded: chain BZ residue 10 SER Chi-restraints excluded: chain B2 residue 10 SER Chi-restraints excluded: chain B6 residue 10 SER Chi-restraints excluded: chain B9 residue 10 SER Chi-restraints excluded: chain CD residue 11 LYS Chi-restraints excluded: chain CH residue 10 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 42 optimal weight: 0.0670 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AQ 2 HIS ** BT 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.173841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.112164 restraints weight = 18041.529| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 5.14 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12816 Z= 0.184 Angle : 0.583 4.188 16128 Z= 0.268 Chirality : 0.065 0.135 1584 Planarity : 0.005 0.038 1728 Dihedral : 10.518 59.245 2592 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.75 % Favored : 79.25 % Rotamer: Outliers : 3.99 % Allowed : 12.67 % Favored : 83.33 % 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: -4.53 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.033 0.002 TYRAQ 3 HIS 0.005 0.000 HISAQ 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (12528) covalent geometry : angle 0.58314 / 0.27 (16128) Misc. bond : bond 0.00059 / 0.04 ( 288) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 TYR cc_start: 0.5791 (m-80) cc_final: 0.4981 (m-80) REVERT: Q 3 TYR cc_start: 0.5754 (m-80) cc_final: 0.5175 (m-80) REVERT: Q 10 SER cc_start: 0.9014 (p) cc_final: 0.8577 (p) REVERT: R 3 TYR cc_start: 0.6076 (m-80) cc_final: 0.5363 (m-80) REVERT: T 10 SER cc_start: 0.8418 (t) cc_final: 0.7798 (m) REVERT: Y 3 TYR cc_start: 0.6274 (OUTLIER) cc_final: 0.5434 (p90) REVERT: Z 3 TYR cc_start: 0.6411 (m-80) cc_final: 0.5757 (p90) REVERT: 0 11 LYS cc_start: 0.8169 (mmtt) cc_final: 0.6543 (ttpt) REVERT: 1 3 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.4096 (p90) REVERT: 3 2 HIS cc_start: 0.3886 (m-70) cc_final: 0.3615 (m90) REVERT: 4 3 TYR cc_start: 0.6423 (m-80) cc_final: 0.6034 (p90) REVERT: 5 5 ILE cc_start: 0.8827 (mt) cc_final: 0.8607 (mp) REVERT: 6 3 TYR cc_start: 0.6827 (m-80) cc_final: 0.6121 (m-80) REVERT: 7 3 TYR cc_start: 0.7394 (m-80) cc_final: 0.6971 (m-80) REVERT: 9 3 TYR cc_start: 0.6826 (m-80) cc_final: 0.6397 (m-80) REVERT: g 10 SER cc_start: 0.8993 (p) cc_final: 0.8702 (p) REVERT: l 2 HIS cc_start: 0.4184 (m90) cc_final: 0.3916 (m-70) REVERT: m 3 TYR cc_start: 0.6198 (m-80) cc_final: 0.5603 (m-80) REVERT: p 3 TYR cc_start: 0.6962 (m-80) cc_final: 0.6684 (m-80) REVERT: q 10 SER cc_start: 0.8925 (p) cc_final: 0.8439 (p) REVERT: AE 3 TYR cc_start: 0.6059 (m-80) cc_final: 0.5783 (m-80) REVERT: AI 10 SER cc_start: 0.8965 (p) cc_final: 0.8538 (p) REVERT: AW 3 TYR cc_start: 0.6234 (m-80) cc_final: 0.5796 (m-10) REVERT: A0 10 SER cc_start: 0.9044 (p) cc_final: 0.8686 (p) REVERT: A1 3 TYR cc_start: 0.6116 (m-80) cc_final: 0.5556 (m-80) REVERT: A7 10 SER cc_start: 0.8815 (p) cc_final: 0.8601 (p) REVERT: BD 3 TYR cc_start: 0.6475 (m-80) cc_final: 0.5968 (m-80) REVERT: BE 3 TYR cc_start: 0.6849 (m-80) cc_final: 0.6539 (m-80) REVERT: BI 10 SER cc_start: 0.8993 (p) cc_final: 0.8559 (p) REVERT: BK 10 SER cc_start: 0.8793 (p) cc_final: 0.8444 (p) REVERT: BT 3 TYR cc_start: 0.6275 (m-80) cc_final: 0.5622 (m-80) REVERT: BU 3 TYR cc_start: 0.6797 (m-80) cc_final: 0.6329 (m-80) REVERT: BZ 3 TYR cc_start: 0.6164 (m-80) cc_final: 0.5793 (m-80) REVERT: B0 10 SER cc_start: 0.9016 (p) cc_final: 0.8579 (p) REVERT: B4 3 TYR cc_start: 0.6885 (m-80) cc_final: 0.6000 (m-80) REVERT: B8 3 TYR cc_start: 0.6503 (OUTLIER) cc_final: 0.4713 (m-80) REVERT: CC 3 TYR cc_start: 0.6200 (m-80) cc_final: 0.5410 (m-80) REVERT: CD 11 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8153 (mtmm) REVERT: CH 3 TYR cc_start: 0.6808 (m-80) cc_final: 0.6597 (m-80) REVERT: CI 3 TYR cc_start: 0.6776 (m-80) cc_final: 0.6376 (m-80) outliers start: 46 outliers final: 41 residues processed: 194 average time/residue: 0.1014 time to fit residues: 30.1108 Evaluate side-chains 213 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain X residue 3 TYR Chi-restraints excluded: chain Y residue 3 TYR Chi-restraints excluded: chain 1 residue 3 TYR Chi-restraints excluded: chain 3 residue 3 TYR Chi-restraints excluded: chain 7 residue 10 SER Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain f residue 3 TYR Chi-restraints excluded: chain g residue 3 TYR Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain o residue 11 LYS Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain w residue 10 SER Chi-restraints excluded: chain y residue 3 TYR Chi-restraints excluded: chain AC residue 10 SER Chi-restraints excluded: chain AD residue 3 TYR Chi-restraints excluded: chain AH residue 10 SER Chi-restraints excluded: chain AK residue 10 SER Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AQ residue 2 HIS Chi-restraints excluded: chain AQ residue 10 SER Chi-restraints excluded: chain AU residue 10 SER Chi-restraints excluded: chain AZ residue 10 SER Chi-restraints excluded: chain A4 residue 10 SER Chi-restraints excluded: chain A6 residue 10 SER Chi-restraints excluded: chain BH residue 10 SER Chi-restraints excluded: chain BO residue 10 SER Chi-restraints excluded: chain BQ residue 10 SER Chi-restraints excluded: chain BZ residue 10 SER Chi-restraints excluded: chain B2 residue 10 SER Chi-restraints excluded: chain B6 residue 10 SER Chi-restraints excluded: chain B7 residue 3 TYR Chi-restraints excluded: chain B8 residue 3 TYR Chi-restraints excluded: chain B9 residue 10 SER Chi-restraints excluded: chain CD residue 11 LYS Chi-restraints excluded: chain CH residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 101 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 143 optimal weight: 0.0870 chunk 64 optimal weight: 0.0030 chunk 47 optimal weight: 5.9990 chunk 11 optimal weight: 0.0570 chunk 106 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 overall best weight: 0.3688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AQ 2 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.179520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.117053 restraints weight = 17703.061| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 5.21 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12816 Z= 0.079 Angle : 0.481 4.493 16128 Z= 0.218 Chirality : 0.061 0.137 1584 Planarity : 0.005 0.041 1728 Dihedral : 9.506 59.212 2592 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.48 % Allowed : 14.93 % Favored : 83.59 % 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: -4.31 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.031 0.002 TYRAQ 3 HIS 0.012 0.000 HISAQ 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.08 (12528) covalent geometry : angle 0.48057 / 0.22 (16128) Misc. bond : bond 0.00015 / 0.01 ( 288) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 SER cc_start: 0.8792 (p) cc_final: 0.8350 (t) REVERT: M 3 TYR cc_start: 0.5693 (m-80) cc_final: 0.4964 (m-80) REVERT: Q 10 SER cc_start: 0.8775 (p) cc_final: 0.8418 (p) REVERT: T 10 SER cc_start: 0.8123 (t) cc_final: 0.7545 (m) REVERT: U 3 TYR cc_start: 0.8051 (m-80) cc_final: 0.7691 (m-80) REVERT: Z 3 TYR cc_start: 0.6464 (m-80) cc_final: 0.5597 (p90) REVERT: 0 11 LYS cc_start: 0.8197 (mmtt) cc_final: 0.6437 (ttpt) REVERT: 3 2 HIS cc_start: 0.3751 (m-70) cc_final: 0.3521 (m90) REVERT: 4 3 TYR cc_start: 0.6263 (m-80) cc_final: 0.5323 (p90) REVERT: 5 5 ILE cc_start: 0.8789 (mt) cc_final: 0.8572 (mp) REVERT: 7 3 TYR cc_start: 0.7271 (m-80) cc_final: 0.6871 (m-80) REVERT: 9 3 TYR cc_start: 0.6793 (m-80) cc_final: 0.6383 (m-80) REVERT: g 10 SER cc_start: 0.8951 (p) cc_final: 0.8684 (p) REVERT: l 2 HIS cc_start: 0.4169 (m90) cc_final: 0.3898 (m-70) REVERT: p 3 TYR cc_start: 0.6895 (m-80) cc_final: 0.6633 (m-80) REVERT: q 10 SER cc_start: 0.8833 (p) cc_final: 0.8366 (p) REVERT: AE 3 TYR cc_start: 0.6006 (m-80) cc_final: 0.5545 (m-80) REVERT: AI 10 SER cc_start: 0.8827 (p) cc_final: 0.8417 (p) REVERT: AJ 3 TYR cc_start: 0.6196 (m-80) cc_final: 0.5972 (m-80) REVERT: AW 3 TYR cc_start: 0.5973 (m-80) cc_final: 0.5424 (m-10) REVERT: A0 10 SER cc_start: 0.8828 (p) cc_final: 0.8509 (p) REVERT: A1 3 TYR cc_start: 0.6030 (m-80) cc_final: 0.5707 (m-80) REVERT: A7 10 SER cc_start: 0.8699 (p) cc_final: 0.8104 (t) REVERT: BD 3 TYR cc_start: 0.6380 (m-80) cc_final: 0.5850 (m-80) REVERT: BE 3 TYR cc_start: 0.6497 (m-80) cc_final: 0.5738 (m-80) REVERT: BI 10 SER cc_start: 0.8811 (p) cc_final: 0.8461 (p) REVERT: BT 3 TYR cc_start: 0.5920 (m-80) cc_final: 0.5483 (m-80) REVERT: B0 10 SER cc_start: 0.8810 (p) cc_final: 0.8420 (p) REVERT: B1 3 TYR cc_start: 0.6261 (m-80) cc_final: 0.5529 (m-80) REVERT: B4 3 TYR cc_start: 0.6767 (m-80) cc_final: 0.5945 (m-80) REVERT: B8 10 SER cc_start: 0.8647 (p) cc_final: 0.8437 (p) REVERT: CC 3 TYR cc_start: 0.5997 (m-80) cc_final: 0.5318 (m-80) REVERT: CD 11 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8061 (mtmm) REVERT: CI 3 TYR cc_start: 0.6771 (m-80) cc_final: 0.6382 (m-80) outliers start: 17 outliers final: 15 residues processed: 179 average time/residue: 0.0995 time to fit residues: 27.3261 Evaluate side-chains 183 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain X residue 3 TYR Chi-restraints excluded: chain 3 residue 3 TYR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain l residue 3 TYR Chi-restraints excluded: chain o residue 11 LYS Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain AD residue 3 TYR Chi-restraints excluded: chain AK residue 10 SER Chi-restraints excluded: chain AO residue 10 SER Chi-restraints excluded: chain AQ residue 10 SER Chi-restraints excluded: chain AV residue 3 TYR Chi-restraints excluded: chain CD residue 11 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 18 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 96 optimal weight: 0.4980 chunk 49 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 2 HIS j 2 HIS ** AQ 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 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 = 0.4806 r_free = 0.4806 target = 0.186681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.109054 restraints weight = 15216.808| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 5.43 r_work: 0.3869 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12816 Z= 0.156 Angle : 0.553 4.228 16128 Z= 0.253 Chirality : 0.064 0.135 1584 Planarity : 0.005 0.040 1728 Dihedral : 9.628 58.375 2592 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.53 % Favored : 82.47 % Rotamer: Outliers : 1.74 % Allowed : 15.10 % Favored : 83.16 % 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: -4.40 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.002 TYR R 3 HIS 0.006 0.000 HIS G 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (12528) covalent geometry : angle 0.55316 / 0.25 (16128) Misc. bond : bond 0.00047 / 0.03 ( 288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2870.01 seconds wall clock time: 50 minutes 23.18 seconds (3023.18 seconds total)