Starting phenix.real_space_refine on Thu Oct 22 22:13:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mfu_48237/10_2026/9mfu_48237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mfu_48237/10_2026/9mfu_48237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mfu_48237/10_2026/9mfu_48237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mfu_48237/10_2026/9mfu_48237.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mfu_48237/10_2026/9mfu_48237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mfu_48237/10_2026/9mfu_48237.map" } resolution = 2.87 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.036 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 5082 2.51 5 N 756 2.21 5 O 938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6776 Number of models: 1 Model: "" Number of chains: 98 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L A 1 " pdbres="PHE A 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7L B 1 " pdbres="PHE B 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L D 1 " pdbres="PHE D 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L E 1 " pdbres="PHE E 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L F 1 " pdbres="PHE F 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L G 1 " pdbres="PHE G 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L X 1 " pdbres="PHE X 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L C 1 " pdbres="PHE C 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7L H 1 " pdbres="PHE H 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L I 1 " pdbres="PHE I 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L J 1 " pdbres="PHE J 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L K 1 " pdbres="PHE K 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L L 1 " pdbres="PHE L 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L M 1 " pdbres="PHE M 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L N 1 " pdbres="PHE N 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7L O 1 " pdbres="PHE O 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L P 1 " pdbres="PHE P 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L Q 1 " pdbres="PHE Q 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L R 1 " pdbres="PHE R 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L S 1 " pdbres="PHE S 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L T 1 " pdbres="PHE T 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L U 1 " pdbres="PHE U 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7L V 1 " pdbres="PHE V 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L W 1 " pdbres="PHE W 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L Y 1 " pdbres="PHE Y 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L Z 1 " pdbres="PHE Z 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L 0 1 " pdbres="PHE 0 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L 1 1 " pdbres="PHE 1 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L 2 1 " pdbres="PHE 2 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7L 3 1 " pdbres="PHE 3 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L 4 1 " pdbres="PHE 4 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L 5 1 " pdbres="PHE 5 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L 6 1 " pdbres="PHE 6 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L 7 1 " pdbres="PHE 7 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L 8 1 " pdbres="PHE 8 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L 9 1 " pdbres="PHE 9 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7L a 1 " pdbres="PHE a 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L b 1 " pdbres="PHE b 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L c 1 " pdbres="PHE c 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L d 1 " pdbres="PHE d 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L e 1 " pdbres="PHE e 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L f 1 " pdbres="PHE f 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L g 1 " pdbres="PHE g 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7L h 1 " pdbres="PHE h 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L i 1 " pdbres="PHE i 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L j 1 " pdbres="PHE j 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L k 1 " pdbres="PHE k 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L l 1 " pdbres="PHE l 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L m 1 " pdbres="PHE m 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L n 1 " pdbres="PHE n 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7L o 1 " pdbres="PHE o 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L p 1 " pdbres="PHE p 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L q 1 " pdbres="PHE q 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L r 1 " pdbres="PHE r 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L s 1 " pdbres="PHE s 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L t 1 " pdbres="PHE t 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L u 1 " pdbres="PHE u 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7L v 1 " pdbres="PHE v 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L w 1 " pdbres="PHE w 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L x 1 " pdbres="PHE x 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L y 1 " pdbres="PHE y 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L z 1 " pdbres="PHE z 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7LAA 1 " pdbres="PHEAA 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAB 1 " pdbres="PHEAB 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AC" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7LAC 1 " pdbres="PHEAC 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AD" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAD 1 " pdbres="PHEAD 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AE" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAE 1 " pdbres="PHEAE 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AF" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7LAF 1 " pdbres="PHEAF 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AG" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAG 1 " pdbres="PHEAG 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AH" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7LAH 1 " pdbres="PHEAH 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AI" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAI 1 " pdbres="PHEAI 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AJ" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7LAJ 1 " pdbres="PHEAJ 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AK" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAK 1 " pdbres="PHEAK 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AL" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAL 1 " pdbres="PHEAL 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7LAM 1 " pdbres="PHEAM 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AN" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAN 1 " pdbres="PHEAN 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AO" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7LAO 1 " pdbres="PHEAO 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AP" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAP 1 " pdbres="PHEAP 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AQ" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7LAQ 1 " pdbres="PHEAQ 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AR" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAR 1 " pdbres="PHEAR 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AS" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAS 1 " pdbres="PHEAS 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AT" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7LAT 1 " pdbres="PHEAT 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AU" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAU 1 " pdbres="PHEAU 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AV" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7LAV 1 " pdbres="PHEAV 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AW" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAW 1 " pdbres="PHEAW 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AX" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7LAX 1 " pdbres="PHEAX 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AY" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAY 1 " pdbres="PHEAY 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AZ" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LAZ 1 " pdbres="PHEAZ 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A0" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7LA0 1 " pdbres="PHEA0 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A1" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LA1 1 " pdbres="PHEA1 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A2" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7LA2 1 " pdbres="PHEA2 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A3" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LA3 1 " pdbres="PHEA3 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'I7L': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="I7LA4 1 " pdbres="PHEA4 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A5" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LA5 1 " pdbres="PHEA5 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A6" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LA6 1 " pdbres="PHEA6 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A7" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7LA7 1 " pdbres="PHEA7 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A8" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7LA8 1 " pdbres="PHEA8 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A9" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7LA9 1 " pdbres="PHEA9 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.45, per 1000 atoms: 0.21 Number of scatterers: 6776 At special positions: 0 Unit cell: (95.2, 97.44, 57.12, 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 938 8.00 N 756 7.00 C 5082 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=98, symmetry=0 Number of additional bonds: simple=98, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 289.4 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 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: 0.53 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.26: 868 1.26 - 1.38: 3266 1.38 - 1.49: 1900 1.49 - 1.61: 1022 1.61 - 1.73: 98 Bond restraints: 7154 Sorted by residual: bond pdb=" C02 I7L j 1 " pdb=" C04 I7L j 1 " ideal model delta sigma weight residual 1.555 1.727 -0.172 2.00e-02 2.50e+03 7.39e+01 bond pdb=" C02 I7LA6 1 " pdb=" C04 I7LA6 1 " ideal model delta sigma weight residual 1.555 1.727 -0.172 2.00e-02 2.50e+03 7.39e+01 bond pdb=" C02 I7L J 1 " pdb=" C04 I7L J 1 " ideal model delta sigma weight residual 1.555 1.727 -0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C02 I7L q 1 " pdb=" C04 I7L q 1 " ideal model delta sigma weight residual 1.555 1.727 -0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C02 I7LAS 1 " pdb=" C04 I7LAS 1 " ideal model delta sigma weight residual 1.555 1.727 -0.172 2.00e-02 2.50e+03 7.38e+01 ... (remaining 7149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.77: 8632 5.77 - 11.55: 566 11.55 - 17.32: 126 17.32 - 23.10: 56 23.10 - 28.87: 84 Bond angle restraints: 9464 Sorted by residual: angle pdb=" C GLY 8 4 " pdb=" N PRO 8 5 " pdb=" CA PRO 8 5 " ideal model delta sigma weight residual 119.78 135.20 -15.42 1.03e+00 9.43e-01 2.24e+02 angle pdb=" C GLYAV 4 " pdb=" N PROAV 5 " pdb=" CA PROAV 5 " ideal model delta sigma weight residual 119.78 135.20 -15.42 1.03e+00 9.43e-01 2.24e+02 angle pdb=" C GLYAA 4 " pdb=" N PROAA 5 " pdb=" CA PROAA 5 " ideal model delta sigma weight residual 119.78 135.18 -15.40 1.03e+00 9.43e-01 2.24e+02 angle pdb=" C GLY T 4 " pdb=" N PRO T 5 " pdb=" CA PRO T 5 " ideal model delta sigma weight residual 119.78 135.18 -15.40 1.03e+00 9.43e-01 2.24e+02 angle pdb=" C GLYAO 4 " pdb=" N PROAO 5 " pdb=" CA PROAO 5 " ideal model delta sigma weight residual 119.78 135.16 -15.38 1.03e+00 9.43e-01 2.23e+02 ... (remaining 9459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.77: 2422 12.77 - 25.53: 294 25.53 - 38.30: 182 38.30 - 51.07: 238 51.07 - 63.83: 70 Dihedral angle restraints: 3206 sinusoidal: 1568 harmonic: 1638 Sorted by residual: dihedral pdb=" N PHEAC 2 " pdb=" C PHEAC 2 " pdb=" CA PHEAC 2 " pdb=" CB PHEAC 2 " ideal model delta harmonic sigma weight residual 122.80 107.33 15.47 0 2.50e+00 1.60e-01 3.83e+01 dihedral pdb=" N PHE V 2 " pdb=" C PHE V 2 " pdb=" CA PHE V 2 " pdb=" CB PHE V 2 " ideal model delta harmonic sigma weight residual 122.80 107.33 15.47 0 2.50e+00 1.60e-01 3.83e+01 dihedral pdb=" N PHEA4 2 " pdb=" C PHEA4 2 " pdb=" CA PHEA4 2 " pdb=" CB PHEA4 2 " ideal model delta harmonic sigma weight residual 122.80 107.34 15.46 0 2.50e+00 1.60e-01 3.83e+01 ... (remaining 3203 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.108: 252 0.108 - 0.215: 140 0.215 - 0.322: 70 0.322 - 0.429: 14 0.429 - 0.537: 42 Chirality restraints: 518 Sorted by residual: chirality pdb=" CA PHE r 3 " pdb=" N PHE r 3 " pdb=" C PHE r 3 " pdb=" CB PHE r 3 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" CA PHE K 3 " pdb=" N PHE K 3 " pdb=" C PHE K 3 " pdb=" CB PHE K 3 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" CA PHEAF 3 " pdb=" N PHEAF 3 " pdb=" C PHEAF 3 " pdb=" CB PHEAF 3 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.10e+00 ... (remaining 515 not shown) Planarity restraints: 1134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE h 2 " 0.025 2.00e-02 2.50e+03 2.22e-02 8.64e+00 pdb=" CG PHE h 2 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE h 2 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE h 2 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE h 2 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE h 2 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE h 2 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEA4 2 " 0.025 2.00e-02 2.50e+03 2.22e-02 8.64e+00 pdb=" CG PHEA4 2 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHEA4 2 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHEA4 2 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHEA4 2 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHEA4 2 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHEA4 2 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEAQ 2 " 0.025 2.00e-02 2.50e+03 2.22e-02 8.61e+00 pdb=" CG PHEAQ 2 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHEAQ 2 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHEAQ 2 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHEAQ 2 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHEAQ 2 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHEAQ 2 " 0.001 2.00e-02 2.50e+03 ... (remaining 1131 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 3936 3.06 - 3.52: 4038 3.52 - 3.98: 7926 3.98 - 4.44: 12658 4.44 - 4.90: 17948 Nonbonded interactions: 46506 Sorted by model distance: nonbonded pdb=" CA GLYA9 4 " pdb=" CD PROA9 5 " model vdw 2.598 3.072 nonbonded pdb=" CA GLY m 4 " pdb=" CD PRO m 5 " model vdw 2.598 3.072 nonbonded pdb=" CA GLYA2 4 " pdb=" CD PROA2 5 " model vdw 2.598 3.072 nonbonded pdb=" CA GLY f 4 " pdb=" CD PRO f 5 " model vdw 2.598 3.072 nonbonded pdb=" CA GLY t 4 " pdb=" CD PRO t 5 " model vdw 2.598 3.072 ... (remaining 46501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 1 through 7) selection = chain '1' selection = (chain '2' and resid 1 through 7) selection = (chain '4' and resid 1 through 7) selection = (chain '5' and resid 1 through 7) selection = chain '6' selection = (chain '7' and resid 1 through 7) selection = chain '8' selection = (chain '9' and resid 1 through 7) selection = (chain 'A' and resid 1 through 7) selection = chain 'A0' selection = (chain 'A1' and resid 1 through 7) selection = chain 'A2' selection = (chain 'A3' and resid 1 through 7) selection = (chain 'A5' and resid 1 through 7) selection = (chain 'A6' and resid 1 through 7) selection = chain 'A7' selection = (chain 'A8' and resid 1 through 7) selection = chain 'A9' selection = chain 'AA' selection = (chain 'AB' and resid 1 through 7) selection = (chain 'AD' and resid 1 through 7) selection = (chain 'AE' and resid 1 through 7) selection = chain 'AF' selection = (chain 'AG' and resid 1 through 7) selection = chain 'AH' selection = (chain 'AI' and resid 1 through 7) selection = (chain 'AK' and resid 1 through 7) selection = (chain 'AL' and resid 1 through 7) selection = chain 'AM' selection = (chain 'AN' and resid 1 through 7) selection = chain 'AO' selection = (chain 'AP' and resid 1 through 7) selection = (chain 'AR' and resid 1 through 7) selection = (chain 'AS' and resid 1 through 7) selection = chain 'AT' selection = (chain 'AU' and resid 1 through 7) selection = chain 'AV' selection = (chain 'AW' and resid 1 through 7) selection = (chain 'AY' and resid 1 through 7) selection = (chain 'AZ' and resid 1 through 7) selection = (chain 'C' and resid 1 through 7) selection = (chain 'D' and resid 1 through 7) selection = (chain 'E' and resid 1 through 7) selection = chain 'F' selection = (chain 'G' and resid 1 through 7) selection = (chain 'I' and resid 1 through 7) selection = (chain 'J' and resid 1 through 7) selection = chain 'K' selection = (chain 'L' and resid 1 through 7) selection = chain 'M' selection = (chain 'N' and resid 1 through 7) selection = (chain 'P' and resid 1 through 7) selection = (chain 'Q' and resid 1 through 7) selection = chain 'R' selection = (chain 'S' and resid 1 through 7) selection = chain 'T' selection = (chain 'U' and resid 1 through 7) selection = (chain 'W' and resid 1 through 7) selection = chain 'X' selection = (chain 'Y' and resid 1 through 7) selection = chain 'Z' selection = (chain 'b' and resid 1 through 7) selection = (chain 'c' and resid 1 through 7) selection = chain 'd' selection = (chain 'e' and resid 1 through 7) selection = chain 'f' selection = (chain 'g' and resid 1 through 7) selection = (chain 'i' and resid 1 through 7) selection = (chain 'j' and resid 1 through 7) selection = chain 'k' selection = (chain 'l' and resid 1 through 7) selection = chain 'm' selection = (chain 'n' and resid 1 through 7) selection = (chain 'p' and resid 1 through 7) selection = (chain 'q' and resid 1 through 7) selection = chain 'r' selection = (chain 's' and resid 1 through 7) selection = chain 't' selection = (chain 'u' and resid 1 through 7) selection = (chain 'w' and resid 1 through 7) selection = (chain 'x' and resid 1 through 7) selection = chain 'y' selection = (chain 'z' and resid 1 through 7) } ncs_group { reference = chain '3' selection = chain 'A4' selection = chain 'AC' selection = chain 'AJ' selection = chain 'AQ' selection = chain 'AX' selection = chain 'B' selection = chain 'H' selection = chain 'O' selection = chain 'V' selection = chain 'a' selection = chain 'h' selection = chain 'o' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.660 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:9.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 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 : 0.042 0.172 7252 Z= 2.291 Angle : 4.253 28.870 9464 Z= 2.126 Chirality : 0.200 0.537 518 Planarity : 0.013 0.071 1134 Dihedral : 21.839 63.831 2170 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % Rotamer: Outliers : 13.51 % Allowed : 5.41 % Favored : 81.08 % Cbeta Deviations : 8.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.20), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.007 TYR 0 7 PHE 0.051 0.009 PHE h 2 Details of bonding type rmsd/Z covalent geometry : bond 0.04216 / 2.30 ( 7154) covalent geometry : angle 4.25345 / 2.13 ( 9464) Misc. bond : bond 0.01755 / 0.97 ( 98) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 112 time to evaluate : 0.186 Fit side-chains REVERT: D 6 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8843 (tt0) REVERT: E 6 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: I 6 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8754 (tt0) REVERT: T 6 GLN cc_start: 0.7137 (tm-30) cc_final: 0.6717 (tm-30) REVERT: W 6 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8947 (tt0) REVERT: 1 6 GLN cc_start: 0.7379 (tm-30) cc_final: 0.7012 (tm-30) REVERT: 5 6 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7967 (mt0) REVERT: c 6 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: p 6 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: AA 6 GLN cc_start: 0.6994 (tm-30) cc_final: 0.6571 (tm-30) REVERT: AH 6 GLN cc_start: 0.7254 (tm-30) cc_final: 0.6867 (tm-30) REVERT: AL 6 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: AS 6 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: AZ 6 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.8053 (mt0) outliers start: 70 outliers final: 27 residues processed: 133 average time/residue: 0.9589 time to fit residues: 131.1261 Evaluate side-chains 151 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain Q residue 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain W residue 6 GLN Chi-restraints excluded: chain Z residue 6 GLN Chi-restraints excluded: chain 4 residue 6 GLN Chi-restraints excluded: chain 5 residue 6 GLN Chi-restraints excluded: chain 6 residue 6 GLN Chi-restraints excluded: chain 9 residue 6 GLN Chi-restraints excluded: chain c residue 6 GLN Chi-restraints excluded: chain d residue 6 GLN Chi-restraints excluded: chain k residue 6 GLN Chi-restraints excluded: chain n residue 6 GLN Chi-restraints excluded: chain p residue 6 GLN Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain u residue 6 GLN Chi-restraints excluded: chain x residue 6 GLN Chi-restraints excluded: chain y residue 6 GLN Chi-restraints excluded: chain AB residue 6 GLN Chi-restraints excluded: chain AF residue 6 GLN Chi-restraints excluded: chain AK residue 6 GLN Chi-restraints excluded: chain AK residue 8 GLN Chi-restraints excluded: chain AL residue 6 GLN Chi-restraints excluded: chain AM residue 6 GLN Chi-restraints excluded: chain AS residue 6 GLN Chi-restraints excluded: chain AT residue 6 GLN Chi-restraints excluded: chain AW residue 6 GLN Chi-restraints excluded: chain AZ residue 6 GLN Chi-restraints excluded: chain A0 residue 6 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN E 6 GLN E 8 GLN C 6 GLN N 6 GLN P 8 GLN Q 6 GLN S 6 GLN U 6 GLN W 8 GLN 0 8 GLN 5 6 GLN b 6 GLN c 6 GLN i 6 GLN i 8 GLN n 6 GLN p 8 GLN u 6 GLN x 6 GLN x 8 GLN z 6 GLN AB 6 GLN AD 8 GLN AE 8 GLN AG 8 GLN AI 6 GLN AL 8 GLN AS 6 GLN AY 6 GLN AZ 6 GLN A5 8 GLN A7 6 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.071564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.063720 restraints weight = 13689.174| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.20 r_work: 0.2769 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7252 Z= 0.133 Angle : 0.840 7.040 9464 Z= 0.399 Chirality : 0.026 0.066 518 Planarity : 0.007 0.044 1134 Dihedral : 16.965 66.218 1007 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 4.25 % Allowed : 13.71 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR Q 7 PHE 0.011 0.001 PHE I 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 ( 7154) covalent geometry : angle 0.84044 / 0.40 ( 9464) Misc. bond : bond 0.00052 / 0.03 ( 98) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.164 Fit side-chains REVERT: G 8 GLN cc_start: 0.8667 (tt0) cc_final: 0.8275 (tt0) REVERT: C 8 GLN cc_start: 0.8538 (tt0) cc_final: 0.8306 (tt0) REVERT: L 8 GLN cc_start: 0.8334 (tt0) cc_final: 0.8133 (tt0) REVERT: U 6 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8711 (tt0) REVERT: 2 8 GLN cc_start: 0.8499 (tt0) cc_final: 0.8191 (tt0) REVERT: l 8 GLN cc_start: 0.8462 (tp-100) cc_final: 0.8094 (tt0) REVERT: AB 6 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: AI 8 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7565 (mt0) REVERT: AL 6 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8424 (mt0) REVERT: AN 8 GLN cc_start: 0.8889 (tt0) cc_final: 0.8518 (tt0) outliers start: 22 outliers final: 8 residues processed: 112 average time/residue: 0.9061 time to fit residues: 104.6869 Evaluate side-chains 123 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain Q residue 6 GLN Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain 9 residue 6 GLN Chi-restraints excluded: chain n residue 6 GLN Chi-restraints excluded: chain u residue 6 GLN Chi-restraints excluded: chain x residue 6 GLN Chi-restraints excluded: chain AB residue 6 GLN Chi-restraints excluded: chain AL residue 6 GLN Chi-restraints excluded: chain AW residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN E 8 GLN C 6 GLN I 8 GLN S 6 GLN 0 6 GLN 7 8 GLN l 6 GLN n 6 GLN u 6 GLN z 6 GLN AB 6 GLN AG 6 GLN AI 6 GLN AL 8 GLN AU 6 GLN AZ 8 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.062047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.053689 restraints weight = 14110.446| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.34 r_work: 0.2566 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.068 7252 Z= 0.602 Angle : 1.108 9.609 9464 Z= 0.561 Chirality : 0.049 0.141 518 Planarity : 0.009 0.048 1134 Dihedral : 20.608 68.505 926 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 0.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 4.05 % Allowed : 11.97 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.20), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.003 TYRA1 7 PHE 0.029 0.003 PHEAF 3 Details of bonding type rmsd/Z covalent geometry : bond 0.01540 / 0.61 ( 7154) covalent geometry : angle 1.10774 / 0.56 ( 9464) Misc. bond : bond 0.00161 / 0.09 ( 98) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.293 Fit side-chains REVERT: L 8 GLN cc_start: 0.8784 (tt0) cc_final: 0.8582 (tt0) REVERT: 2 8 GLN cc_start: 0.8896 (tt0) cc_final: 0.8690 (tt0) REVERT: AP 8 GLN cc_start: 0.8785 (tt0) cc_final: 0.8518 (tt0) REVERT: A3 8 GLN cc_start: 0.8750 (tp40) cc_final: 0.8352 (tm-30) outliers start: 21 outliers final: 11 residues processed: 101 average time/residue: 0.9907 time to fit residues: 103.0828 Evaluate side-chains 110 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain 9 residue 6 GLN Chi-restraints excluded: chain c residue 6 GLN Chi-restraints excluded: chain n residue 6 GLN Chi-restraints excluded: chain u residue 6 GLN Chi-restraints excluded: chain AB residue 6 GLN Chi-restraints excluded: chain AK residue 8 GLN Chi-restraints excluded: chain AW residue 6 GLN Chi-restraints excluded: chain AZ residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN E 8 GLN S 6 GLN U 6 GLN l 6 GLN w 8 GLN z 6 GLN AI 6 GLN AL 8 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.068547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.059820 restraints weight = 13569.328| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.41 r_work: 0.2708 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7252 Z= 0.113 Angle : 0.712 6.306 9464 Z= 0.334 Chirality : 0.026 0.078 518 Planarity : 0.009 0.044 1134 Dihedral : 13.403 59.883 917 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 3.28 % Allowed : 13.71 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR S 7 PHE 0.008 0.001 PHE H 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.11 ( 7154) covalent geometry : angle 0.71215 / 0.33 ( 9464) Misc. bond : bond 0.00045 / 0.02 ( 98) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.246 Fit side-chains REVERT: 2 8 GLN cc_start: 0.8644 (tt0) cc_final: 0.8376 (tt0) REVERT: 7 8 GLN cc_start: 0.8544 (tt0) cc_final: 0.8278 (tt0) REVERT: 9 6 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: b 8 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7357 (mt0) REVERT: l 8 GLN cc_start: 0.8464 (tp-100) cc_final: 0.7889 (tt0) REVERT: AI 8 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7692 (tt0) REVERT: AP 8 GLN cc_start: 0.8538 (tt0) cc_final: 0.8197 (tt0) REVERT: AS 8 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.8029 (tp-100) REVERT: AW 6 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: A3 8 GLN cc_start: 0.8649 (tp40) cc_final: 0.8363 (mm-40) outliers start: 17 outliers final: 8 residues processed: 112 average time/residue: 0.8821 time to fit residues: 101.9608 Evaluate side-chains 121 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 9 residue 6 GLN Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain e residue 8 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain n residue 6 GLN Chi-restraints excluded: chain u residue 6 GLN Chi-restraints excluded: chain AB residue 6 GLN Chi-restraints excluded: chain AS residue 8 GLN Chi-restraints excluded: chain AW residue 6 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN E 8 GLN J 6 GLN P 8 GLN Q 6 GLN S 6 GLN 4 8 GLN 7 6 GLN 7 8 GLN l 6 GLN w 8 GLN z 6 GLN AG 6 GLN AI 6 GLN AL 8 GLN AU 6 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.061910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.053500 restraints weight = 14272.854| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.41 r_work: 0.2562 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9196 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.071 7252 Z= 0.606 Angle : 1.065 9.256 9464 Z= 0.534 Chirality : 0.049 0.146 518 Planarity : 0.009 0.048 1134 Dihedral : 20.329 66.640 917 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 4.25 % Allowed : 13.90 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.26), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.20), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR z 7 PHE 0.027 0.003 PHEAT 3 Details of bonding type rmsd/Z covalent geometry : bond 0.01550 / 0.61 ( 7154) covalent geometry : angle 1.06469 / 0.53 ( 9464) Misc. bond : bond 0.00172 / 0.10 ( 98) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.253 Fit side-chains REVERT: D 6 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8994 (tt0) REVERT: L 8 GLN cc_start: 0.8861 (tt0) cc_final: 0.8566 (tt0) REVERT: P 8 GLN cc_start: 0.7705 (mt0) cc_final: 0.7489 (mt0) REVERT: 2 8 GLN cc_start: 0.8914 (tt0) cc_final: 0.8705 (tt0) REVERT: 9 6 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: b 8 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7375 (mt0) REVERT: m 6 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7662 (tm-30) REVERT: p 8 GLN cc_start: 0.8304 (mt0) cc_final: 0.7840 (mt0) REVERT: AK 6 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.9043 (tt0) REVERT: AW 6 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: A3 8 GLN cc_start: 0.8775 (tp40) cc_final: 0.8173 (tm-30) outliers start: 22 outliers final: 11 residues processed: 105 average time/residue: 0.9388 time to fit residues: 101.5607 Evaluate side-chains 119 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 9 residue 6 GLN Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain c residue 6 GLN Chi-restraints excluded: chain e residue 8 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain n residue 6 GLN Chi-restraints excluded: chain u residue 6 GLN Chi-restraints excluded: chain AB residue 6 GLN Chi-restraints excluded: chain AK residue 6 GLN Chi-restraints excluded: chain AS residue 8 GLN Chi-restraints excluded: chain AW residue 6 GLN Chi-restraints excluded: chain AZ residue 6 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN E 8 GLN S 6 GLN 4 8 GLN c 8 GLN l 6 GLN n 8 GLN w 8 GLN z 6 GLN AI 6 GLN AL 8 GLN AR 8 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.068112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.059487 restraints weight = 13667.989| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.41 r_work: 0.2706 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7252 Z= 0.110 Angle : 0.698 6.397 9464 Z= 0.327 Chirality : 0.026 0.078 518 Planarity : 0.009 0.047 1134 Dihedral : 13.453 59.763 917 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.24 % Favored : 84.76 % Rotamer: Outliers : 3.47 % Allowed : 14.86 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR g 7 PHE 0.008 0.001 PHE H 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.11 ( 7154) covalent geometry : angle 0.69761 / 0.33 ( 9464) Misc. bond : bond 0.00049 / 0.03 ( 98) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.283 Fit side-chains REVERT: L 8 GLN cc_start: 0.8549 (tt0) cc_final: 0.8221 (tt0) REVERT: 2 8 GLN cc_start: 0.8655 (tt0) cc_final: 0.8393 (tt0) REVERT: 9 6 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: b 8 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7234 (mt0) REVERT: l 8 GLN cc_start: 0.8601 (tp-100) cc_final: 0.7972 (tt0) REVERT: AG 6 GLN cc_start: 0.8693 (mt0) cc_final: 0.8439 (mt0) REVERT: AW 6 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: A3 8 GLN cc_start: 0.8663 (tp40) cc_final: 0.8349 (mm-40) outliers start: 18 outliers final: 11 residues processed: 110 average time/residue: 0.8800 time to fit residues: 99.7624 Evaluate side-chains 122 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 9 residue 6 GLN Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain e residue 8 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain n residue 6 GLN Chi-restraints excluded: chain u residue 6 GLN Chi-restraints excluded: chain AB residue 6 GLN Chi-restraints excluded: chain AW residue 6 GLN Chi-restraints excluded: chain AZ residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN E 8 GLN Q 6 GLN Q 8 GLN S 6 GLN 4 8 GLN 7 6 GLN c 8 GLN j 6 GLN l 6 GLN w 8 GLN z 6 GLN AI 6 GLN AL 8 GLN AU 6 GLN AU 8 GLN AZ 8 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.061868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.053497 restraints weight = 14108.660| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.40 r_work: 0.2567 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9194 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.074 7252 Z= 0.603 Angle : 1.052 9.183 9464 Z= 0.526 Chirality : 0.049 0.147 518 Planarity : 0.009 0.049 1134 Dihedral : 20.316 66.764 917 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 4.25 % Allowed : 14.67 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.26), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.20), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYRA1 7 PHE 0.027 0.003 PHE 6 3 Details of bonding type rmsd/Z covalent geometry : bond 0.01541 / 0.61 ( 7154) covalent geometry : angle 1.05159 / 0.53 ( 9464) Misc. bond : bond 0.00164 / 0.09 ( 98) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.276 Fit side-chains REVERT: D 6 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.9020 (tt0) REVERT: P 8 GLN cc_start: 0.7750 (mt0) cc_final: 0.7473 (mt0) REVERT: 2 8 GLN cc_start: 0.8921 (tt0) cc_final: 0.8716 (tt0) REVERT: 9 6 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: b 8 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7387 (mt0) REVERT: m 6 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7672 (tm-30) REVERT: AW 6 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: A3 8 GLN cc_start: 0.8790 (tp40) cc_final: 0.8213 (tm-30) outliers start: 22 outliers final: 13 residues processed: 104 average time/residue: 0.9683 time to fit residues: 103.7070 Evaluate side-chains 120 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain 5 residue 6 GLN Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 9 residue 6 GLN Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain c residue 6 GLN Chi-restraints excluded: chain e residue 8 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain n residue 6 GLN Chi-restraints excluded: chain u residue 6 GLN Chi-restraints excluded: chain AB residue 6 GLN Chi-restraints excluded: chain AW residue 6 GLN Chi-restraints excluded: chain AZ residue 6 GLN Chi-restraints excluded: chain A1 residue 8 GLN Chi-restraints excluded: chain A3 residue 6 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN D 8 GLN E 8 GLN G 8 GLN Q 6 GLN S 6 GLN 4 8 GLN c 8 GLN l 6 GLN n 8 GLN z 6 GLN AL 8 GLN AU 6 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.067359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.058780 restraints weight = 13723.044| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.42 r_work: 0.2693 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7252 Z= 0.118 Angle : 0.707 6.494 9464 Z= 0.335 Chirality : 0.027 0.080 518 Planarity : 0.009 0.047 1134 Dihedral : 13.812 59.721 917 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.24 % Favored : 84.76 % Rotamer: Outliers : 2.51 % Allowed : 16.60 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR g 7 PHE 0.008 0.001 PHE o 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.12 ( 7154) covalent geometry : angle 0.70700 / 0.33 ( 9464) Misc. bond : bond 0.00032 / 0.02 ( 98) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.177 Fit side-chains REVERT: L 8 GLN cc_start: 0.8545 (tt0) cc_final: 0.8239 (tt0) REVERT: U 8 GLN cc_start: 0.8246 (tt0) cc_final: 0.8020 (tt0) REVERT: 2 8 GLN cc_start: 0.8666 (tt0) cc_final: 0.8422 (tt0) REVERT: 9 6 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: b 8 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7266 (mt0) REVERT: l 8 GLN cc_start: 0.8576 (tp-100) cc_final: 0.7920 (tp40) REVERT: p 8 GLN cc_start: 0.8308 (mt0) cc_final: 0.7987 (mt0) REVERT: AW 6 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: A3 8 GLN cc_start: 0.8681 (tp40) cc_final: 0.8351 (mm-40) outliers start: 13 outliers final: 9 residues processed: 107 average time/residue: 0.9091 time to fit residues: 100.2416 Evaluate side-chains 118 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 9 residue 6 GLN Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain e residue 8 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain n residue 6 GLN Chi-restraints excluded: chain AB residue 6 GLN Chi-restraints excluded: chain AW residue 6 GLN Chi-restraints excluded: chain AZ residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN E 8 GLN P 8 GLN Q 6 GLN S 6 GLN 4 8 GLN 7 6 GLN c 8 GLN l 6 GLN w 8 GLN z 6 GLN AL 8 GLN AN 8 GLN AU 6 GLN AU 8 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.061860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.053463 restraints weight = 14360.251| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.42 r_work: 0.2567 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9196 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.073 7252 Z= 0.603 Angle : 1.050 9.136 9464 Z= 0.525 Chirality : 0.049 0.146 518 Planarity : 0.010 0.049 1134 Dihedral : 20.128 66.687 914 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.14 % Favored : 82.86 % Rotamer: Outliers : 3.47 % Allowed : 15.83 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.26), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.20), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.002 TYRA1 7 PHE 0.027 0.003 PHE 6 3 Details of bonding type rmsd/Z covalent geometry : bond 0.01541 / 0.61 ( 7154) covalent geometry : angle 1.05030 / 0.53 ( 9464) Misc. bond : bond 0.00161 / 0.09 ( 98) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.151 Fit side-chains REVERT: D 6 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.9041 (tt0) REVERT: P 8 GLN cc_start: 0.7809 (mt0) cc_final: 0.7607 (mt0) REVERT: 9 6 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: b 8 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7426 (mt0) REVERT: m 6 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7679 (tm-30) REVERT: AW 6 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8551 (tt0) REVERT: A3 8 GLN cc_start: 0.8778 (tp40) cc_final: 0.8209 (tm-30) outliers start: 18 outliers final: 10 residues processed: 103 average time/residue: 0.9651 time to fit residues: 102.4342 Evaluate side-chains 115 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 9 residue 6 GLN Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain c residue 6 GLN Chi-restraints excluded: chain e residue 8 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain n residue 6 GLN Chi-restraints excluded: chain AB residue 6 GLN Chi-restraints excluded: chain AW residue 6 GLN Chi-restraints excluded: chain AZ residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN E 8 GLN Q 6 GLN S 6 GLN 0 8 GLN 4 8 GLN 7 6 GLN c 8 GLN l 6 GLN n 8 GLN w 8 GLN z 6 GLN AL 8 GLN AS 8 GLN AU 6 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.067766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.059235 restraints weight = 13659.938| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.40 r_work: 0.2703 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7252 Z= 0.114 Angle : 0.700 6.332 9464 Z= 0.331 Chirality : 0.026 0.076 518 Planarity : 0.009 0.047 1134 Dihedral : 13.101 59.758 914 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.48 % Favored : 84.52 % Rotamer: Outliers : 2.12 % Allowed : 16.99 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR 2 7 PHE 0.008 0.001 PHE H 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.11 ( 7154) covalent geometry : angle 0.69960 / 0.33 ( 9464) Misc. bond : bond 0.00027 / 0.01 ( 98) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.169 Fit side-chains REVERT: L 8 GLN cc_start: 0.8514 (tt0) cc_final: 0.8225 (tt0) REVERT: 9 6 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8430 (tt0) REVERT: b 8 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7260 (mt0) REVERT: l 8 GLN cc_start: 0.8565 (tp-100) cc_final: 0.7817 (tp40) REVERT: AW 6 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8589 (tt0) REVERT: A3 8 GLN cc_start: 0.8649 (tp40) cc_final: 0.8318 (mm-40) outliers start: 11 outliers final: 8 residues processed: 108 average time/residue: 0.8581 time to fit residues: 95.6690 Evaluate side-chains 118 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain 9 residue 6 GLN Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain c residue 6 GLN Chi-restraints excluded: chain e residue 8 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain AB residue 6 GLN Chi-restraints excluded: chain AB residue 8 GLN Chi-restraints excluded: chain AW residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN E 8 GLN P 8 GLN Q 6 GLN S 6 GLN 0 8 GLN 4 8 GLN 7 6 GLN ** 7 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 8 GLN w 8 GLN z 6 GLN AE 6 GLN AI 6 GLN AL 8 GLN AN 8 GLN AU 6 GLN A8 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.061953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.053597 restraints weight = 14329.166| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.42 r_work: 0.2568 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9196 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.072 7252 Z= 0.601 Angle : 1.046 9.057 9464 Z= 0.523 Chirality : 0.049 0.148 518 Planarity : 0.010 0.049 1134 Dihedral : 19.845 66.321 911 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.38 % Favored : 82.62 % Rotamer: Outliers : 2.70 % Allowed : 16.80 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.26), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.20), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.002 TYRA1 7 PHE 0.026 0.003 PHEAT 3 Details of bonding type rmsd/Z covalent geometry : bond 0.01536 / 0.61 ( 7154) covalent geometry : angle 1.04617 / 0.52 ( 9464) Misc. bond : bond 0.00161 / 0.09 ( 98) =============================================================================== Job complete usr+sys time: 2230.51 seconds wall clock time: 38 minutes 34.13 seconds (2314.13 seconds total)