Starting phenix.real_space_refine on Wed Sep 17 06:50:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mfu_48237/09_2025/9mfu_48237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mfu_48237/09_2025/9mfu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mfu_48237/09_2025/9mfu_48237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mfu_48237/09_2025/9mfu_48237.map" model { file = "/net/cci-nas-00/data/ceres_data/9mfu_48237/09_2025/9mfu_48237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mfu_48237/09_2025/9mfu_48237.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 1.75, per 1000 atoms: 0.26 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: 0.54 Conformation dependent library (CDL) restraints added in 162.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.50 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: 0.71 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.770 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.010 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:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 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 aren 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 covalent geometry : bond 0.04216 ( 7154) covalent geometry : angle 4.25345 ( 9464) Misc. bond : bond 0.01755 ( 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 : 0.253 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: 0.7138 (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: 0.8475 (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: 1.0201 time to fit residues: 139.3971 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 : 0.247 ------------------------------------------------------------------------------- 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: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN D 8 GLN E 6 GLN E 8 GLN P 8 GLN Q 6 GLN S 6 GLN W 8 GLN 4 8 GLN 5 6 GLN 7 6 GLN b 6 GLN c 6 GLN i 6 GLN i 8 GLN l 6 GLN p 6 GLN p 8 GLN w 8 GLN x 6 GLN x 8 GLN z 6 GLN AD 8 GLN AE 8 GLN AI 6 GLN AK 8 GLN AL 6 GLN AL 8 GLN AR 8 GLN AS 6 GLN AU 6 GLN AY 6 GLN AZ 6 GLN A5 8 GLN A7 6 GLN A8 6 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.050887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.043151 restraints weight = 17889.312| |-----------------------------------------------------------------------------| r_work (start): 0.2433 rms_B_bonded: 2.44 r_work: 0.2298 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2177 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9272 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.101 0.495 7252 Z= 4.018 Angle : 3.577 26.344 9464 Z= 1.868 Chirality : 0.243 0.598 518 Planarity : 0.021 0.091 1134 Dihedral : 27.875 89.312 1007 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.67 % Favored : 78.33 % Rotamer: Outliers : 8.88 % Allowed : 10.81 % Favored : 80.31 % Cbeta Deviations : 7.53 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.03 (0.20), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.59 (0.15), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.053 0.012 TYR z 7 PHE 0.073 0.013 PHE K 3 Details of bonding type rmsd covalent geometry : bond 0.10171 ( 7154) covalent geometry : angle 3.57651 ( 9464) Misc. bond : bond 0.00841 ( 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 150 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.166 Fit side-chains REVERT: E 8 GLN cc_start: 0.8765 (mt0) cc_final: 0.7598 (tm-30) REVERT: F 6 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8854 (mt0) REVERT: J 8 GLN cc_start: 0.8974 (mt0) cc_final: 0.7565 (tm-30) REVERT: K 6 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8338 (tm130) REVERT: L 8 GLN cc_start: 0.9240 (tt0) cc_final: 0.8911 (tt0) REVERT: M 6 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8116 (pm20) REVERT: Y 8 GLN cc_start: 0.9000 (mt0) cc_final: 0.7748 (tm130) REVERT: Z 6 GLN cc_start: 0.9166 (tt0) cc_final: 0.7666 (tm130) REVERT: 1 6 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8000 (tm130) REVERT: 5 8 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: 9 8 GLN cc_start: 0.8987 (tt0) cc_final: 0.8218 (tm-30) REVERT: c 8 GLN cc_start: 0.8464 (mt0) cc_final: 0.7428 (tm-30) REVERT: d 6 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7991 (tm130) REVERT: j 8 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: k 6 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.7935 (tm130) REVERT: m 6 GLN cc_start: 0.8686 (tm-30) cc_final: 0.7961 (tm-30) REVERT: q 8 GLN cc_start: 0.8859 (mt0) cc_final: 0.7643 (tm-30) REVERT: r 6 GLN cc_start: 0.8999 (tt0) cc_final: 0.8372 (tm130) REVERT: x 8 GLN cc_start: 0.9017 (mt0) cc_final: 0.7481 (tm-30) REVERT: AB 8 GLN cc_start: 0.8624 (tt0) cc_final: 0.8380 (tm-30) REVERT: AE 8 GLN cc_start: 0.8816 (mt0) cc_final: 0.7253 (tm-30) REVERT: AF 6 GLN cc_start: 0.9267 (tt0) cc_final: 0.7843 (tm130) REVERT: AH 6 GLN cc_start: 0.8542 (tm-30) cc_final: 0.7791 (tm130) REVERT: AK 8 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: AL 8 GLN cc_start: 0.8734 (mt0) cc_final: 0.7412 (tm-30) REVERT: AP 8 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8523 (tm-30) REVERT: AS 8 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: AY 2 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.9047 (t80) REVERT: AY 8 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7723 (tp40) REVERT: AZ 8 GLN cc_start: 0.8390 (mt0) cc_final: 0.7476 (tm-30) REVERT: A6 8 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: A9 6 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8032 (tm130) outliers start: 46 outliers final: 13 residues processed: 113 average time/residue: 0.9708 time to fit residues: 112.9980 Evaluate side-chains 128 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain 4 residue 2 PHE Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 6 residue 6 GLN Chi-restraints excluded: chain 9 residue 6 GLN Chi-restraints excluded: chain d residue 6 GLN Chi-restraints excluded: chain j residue 6 GLN Chi-restraints excluded: chain j residue 8 GLN Chi-restraints excluded: chain k residue 6 GLN Chi-restraints excluded: chain p residue 2 PHE Chi-restraints excluded: chain AD residue 2 PHE Chi-restraints excluded: chain AK residue 8 GLN Chi-restraints excluded: chain AP residue 8 GLN Chi-restraints excluded: chain AR residue 2 PHE Chi-restraints excluded: chain AS residue 8 GLN Chi-restraints excluded: chain AW residue 6 GLN Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AY residue 8 GLN Chi-restraints excluded: chain A0 residue 6 GLN Chi-restraints excluded: chain A6 residue 6 GLN Chi-restraints excluded: chain A6 residue 8 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN I 8 GLN Q 8 GLN S 6 GLN 4 8 GLN 7 8 GLN p 8 GLN x 6 GLN z 6 GLN AU 6 GLN A7 6 GLN A8 6 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.050527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.042784 restraints weight = 17667.974| |-----------------------------------------------------------------------------| r_work (start): 0.2430 rms_B_bonded: 2.44 r_work: 0.2293 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2172 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9275 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.101 0.484 7252 Z= 4.033 Angle : 3.565 25.863 9464 Z= 1.863 Chirality : 0.242 0.608 518 Planarity : 0.021 0.101 1134 Dihedral : 26.842 87.381 926 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 26.19 % Favored : 73.57 % Rotamer: Outliers : 9.46 % Allowed : 12.55 % Favored : 77.99 % Cbeta Deviations : 8.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.06 % Twisted General : 1.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.44 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.91 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.060 0.012 TYR g 7 PHE 0.087 0.013 PHE K 3 Details of bonding type rmsd covalent geometry : bond 0.10197 ( 7154) covalent geometry : angle 3.56516 ( 9464) Misc. bond : bond 0.00815 ( 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 150 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 101 time to evaluate : 0.281 Fit side-chains REVERT: E 8 GLN cc_start: 0.8732 (mt0) cc_final: 0.7477 (tm-30) REVERT: K 6 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8263 (tm130) REVERT: M 6 GLN cc_start: 0.8820 (tm-30) cc_final: 0.7892 (pp30) REVERT: U 8 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8374 (tm-30) REVERT: Y 8 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7735 (tm130) REVERT: Z 6 GLN cc_start: 0.9147 (tt0) cc_final: 0.7896 (tm130) REVERT: 1 6 GLN cc_start: 0.8682 (tm-30) cc_final: 0.7940 (tm130) REVERT: 5 8 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: 9 8 GLN cc_start: 0.9034 (tt0) cc_final: 0.8307 (tm-30) REVERT: c 8 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: j 8 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: m 6 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8047 (tm-30) REVERT: q 8 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: r 6 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8459 (tm130) REVERT: u 8 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8347 (tp40) REVERT: AE 8 GLN cc_start: 0.8840 (mt0) cc_final: 0.7207 (tm-30) REVERT: AF 6 GLN cc_start: 0.9257 (tt0) cc_final: 0.7780 (tm130) REVERT: AH 6 GLN cc_start: 0.8568 (tm-30) cc_final: 0.7742 (tm130) REVERT: AK 8 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: AL 8 GLN cc_start: 0.8711 (mt0) cc_final: 0.7385 (tm-30) REVERT: AP 8 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8783 (tm-30) REVERT: AS 8 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: AY 8 GLN cc_start: 0.8012 (mt0) cc_final: 0.7763 (tp40) REVERT: AZ 8 GLN cc_start: 0.8453 (mt0) cc_final: 0.7602 (tm-30) REVERT: A3 8 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8737 (tm-30) REVERT: A6 8 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: A9 6 GLN cc_start: 0.8751 (tm-30) cc_final: 0.7849 (tm-30) outliers start: 49 outliers final: 18 residues processed: 114 average time/residue: 0.9500 time to fit residues: 111.5806 Evaluate side-chains 129 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain Y residue 8 GLN Chi-restraints excluded: chain 4 residue 2 PHE Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 6 residue 6 GLN Chi-restraints excluded: chain c residue 8 GLN Chi-restraints excluded: chain d residue 6 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain j residue 6 GLN Chi-restraints excluded: chain j residue 8 GLN Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain p residue 2 PHE Chi-restraints excluded: chain q residue 5 PRO Chi-restraints excluded: chain q residue 8 GLN Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain u residue 8 GLN Chi-restraints excluded: chain AD residue 2 PHE Chi-restraints excluded: chain AK residue 8 GLN Chi-restraints excluded: chain AP residue 8 GLN Chi-restraints excluded: chain AR residue 2 PHE Chi-restraints excluded: chain AS residue 8 GLN Chi-restraints excluded: chain AW residue 6 GLN Chi-restraints excluded: chain A0 residue 6 GLN Chi-restraints excluded: chain A1 residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Chi-restraints excluded: chain A6 residue 6 GLN Chi-restraints excluded: chain A6 residue 8 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN I 8 GLN L 8 GLN Q 8 GLN S 6 GLN 0 8 GLN 4 8 GLN x 6 GLN z 6 GLN AG 6 GLN A8 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.050404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.042717 restraints weight = 17780.067| |-----------------------------------------------------------------------------| r_work (start): 0.2424 rms_B_bonded: 2.44 r_work: 0.2285 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2163 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9277 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 : 0.101 0.468 7252 Z= 4.041 Angle : 3.563 26.429 9464 Z= 1.859 Chirality : 0.242 0.600 518 Planarity : 0.021 0.102 1134 Dihedral : 26.262 87.583 917 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 25.00 % Favored : 74.76 % Rotamer: Outliers : 9.46 % Allowed : 14.09 % Favored : 76.45 % Cbeta Deviations : 8.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 1.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.48 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.066 0.012 TYR g 7 PHE 0.089 0.013 PHE K 3 Details of bonding type rmsd covalent geometry : bond 0.10214 ( 7154) covalent geometry : angle 3.56277 ( 9464) Misc. bond : bond 0.00815 ( 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 148 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 99 time to evaluate : 0.249 Fit side-chains REVERT: E 8 GLN cc_start: 0.8743 (mt0) cc_final: 0.7504 (tm-30) REVERT: J 8 GLN cc_start: 0.9021 (mt0) cc_final: 0.7569 (tm-30) REVERT: K 6 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8265 (tm130) REVERT: U 8 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: Y 8 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: 1 6 GLN cc_start: 0.8662 (tm-30) cc_final: 0.7912 (tm130) REVERT: 5 8 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: 9 6 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8439 (tp40) REVERT: 9 8 GLN cc_start: 0.9051 (tt0) cc_final: 0.8283 (tm-30) REVERT: c 8 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: j 8 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: m 6 GLN cc_start: 0.8786 (tm-30) cc_final: 0.7985 (tm-30) REVERT: q 8 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: r 6 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8469 (tm130) REVERT: u 8 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8570 (tp-100) REVERT: AE 8 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: AF 6 GLN cc_start: 0.9259 (tt0) cc_final: 0.7761 (tm130) REVERT: AH 6 GLN cc_start: 0.8597 (tm-30) cc_final: 0.7740 (tm130) REVERT: AK 8 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: AL 8 GLN cc_start: 0.8772 (mt0) cc_final: 0.7395 (tm-30) REVERT: AP 8 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8782 (tm-30) REVERT: AS 8 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: AY 2 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.9151 (t80) REVERT: AZ 8 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: A3 8 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8508 (tm-30) REVERT: A6 8 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: A9 6 GLN cc_start: 0.8771 (tm-30) cc_final: 0.7880 (tm-30) outliers start: 49 outliers final: 19 residues processed: 108 average time/residue: 0.9651 time to fit residues: 107.1707 Evaluate side-chains 133 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain Y residue 8 GLN Chi-restraints excluded: chain 4 residue 2 PHE Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 6 residue 6 GLN Chi-restraints excluded: chain 9 residue 6 GLN Chi-restraints excluded: chain c residue 8 GLN Chi-restraints excluded: chain d residue 6 GLN Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain j residue 6 GLN Chi-restraints excluded: chain j residue 8 GLN Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain p residue 2 PHE Chi-restraints excluded: chain q residue 8 GLN Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain u residue 8 GLN Chi-restraints excluded: chain AD residue 2 PHE Chi-restraints excluded: chain AE residue 8 GLN Chi-restraints excluded: chain AK residue 8 GLN Chi-restraints excluded: chain AP residue 6 GLN Chi-restraints excluded: chain AP residue 8 GLN Chi-restraints excluded: chain AR residue 2 PHE Chi-restraints excluded: chain AS residue 8 GLN Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AZ residue 8 GLN Chi-restraints excluded: chain A0 residue 6 GLN Chi-restraints excluded: chain A1 residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Chi-restraints excluded: chain A6 residue 6 GLN Chi-restraints excluded: chain A6 residue 8 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN I 6 GLN I 8 GLN L 8 GLN Q 8 GLN S 6 GLN 0 8 GLN 4 8 GLN x 6 GLN z 6 GLN AG 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.050315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.042576 restraints weight = 18145.321| |-----------------------------------------------------------------------------| r_work (start): 0.2425 rms_B_bonded: 2.46 r_work: 0.2287 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2163 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9279 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.102 0.469 7252 Z= 4.044 Angle : 3.573 26.367 9464 Z= 1.863 Chirality : 0.244 0.600 518 Planarity : 0.021 0.104 1134 Dihedral : 26.214 87.538 914 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 26.90 % Favored : 72.86 % Rotamer: Outliers : 9.27 % Allowed : 14.09 % Favored : 76.64 % Cbeta Deviations : 8.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 1.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.53 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.97 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.069 0.012 TYR g 7 PHE 0.091 0.013 PHE K 3 Details of bonding type rmsd covalent geometry : bond 0.10220 ( 7154) covalent geometry : angle 3.57329 ( 9464) Misc. bond : bond 0.00834 ( 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 145 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 97 time to evaluate : 0.187 Fit side-chains REVERT: E 8 GLN cc_start: 0.8742 (mt0) cc_final: 0.7468 (tm-30) REVERT: J 8 GLN cc_start: 0.9026 (mt0) cc_final: 0.7567 (tm-30) REVERT: K 6 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8259 (tm130) REVERT: R 6 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7941 (tm130) REVERT: U 8 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: Y 8 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7745 (tm130) REVERT: Z 6 GLN cc_start: 0.9184 (tt0) cc_final: 0.7972 (tm130) REVERT: 1 6 GLN cc_start: 0.8688 (tm-30) cc_final: 0.7919 (tm130) REVERT: 5 8 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: 9 8 GLN cc_start: 0.9032 (tt0) cc_final: 0.8269 (tm-30) REVERT: c 8 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: j 8 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: m 6 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: q 8 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: r 6 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8485 (tm130) REVERT: u 8 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: x 8 GLN cc_start: 0.9067 (mt0) cc_final: 0.7674 (tm-30) REVERT: AB 8 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8561 (tm-30) REVERT: AE 8 GLN cc_start: 0.8875 (mt0) cc_final: 0.7201 (tm-30) REVERT: AF 6 GLN cc_start: 0.9276 (tt0) cc_final: 0.7770 (tm130) REVERT: AH 6 GLN cc_start: 0.8620 (tm-30) cc_final: 0.7789 (tm130) REVERT: AI 8 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: AK 8 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: AL 8 GLN cc_start: 0.8773 (mt0) cc_final: 0.7413 (tm-30) REVERT: AP 8 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8938 (tm-30) REVERT: AS 8 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: AW 6 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8559 (tp40) REVERT: AY 8 GLN cc_start: 0.8138 (mt0) cc_final: 0.7781 (mt0) REVERT: AZ 8 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: A3 8 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8607 (tm-30) REVERT: A6 8 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: A9 6 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7889 (tm-30) outliers start: 48 outliers final: 20 residues processed: 108 average time/residue: 0.9370 time to fit residues: 104.1769 Evaluate side-chains 137 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain Y residue 8 GLN Chi-restraints excluded: chain 2 residue 6 GLN Chi-restraints excluded: chain 4 residue 2 PHE Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 6 residue 6 GLN Chi-restraints excluded: chain c residue 8 GLN Chi-restraints excluded: chain d residue 6 GLN Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain j residue 6 GLN Chi-restraints excluded: chain j residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain p residue 2 PHE Chi-restraints excluded: chain q residue 5 PRO Chi-restraints excluded: chain q residue 8 GLN Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain u residue 8 GLN Chi-restraints excluded: chain AB residue 8 GLN Chi-restraints excluded: chain AD residue 2 PHE Chi-restraints excluded: chain AI residue 8 GLN Chi-restraints excluded: chain AK residue 8 GLN Chi-restraints excluded: chain AP residue 6 GLN Chi-restraints excluded: chain AP residue 8 GLN Chi-restraints excluded: chain AR residue 2 PHE Chi-restraints excluded: chain AS residue 8 GLN Chi-restraints excluded: chain AW residue 6 GLN Chi-restraints excluded: chain AZ residue 8 GLN Chi-restraints excluded: chain A0 residue 6 GLN Chi-restraints excluded: chain A1 residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Chi-restraints excluded: chain A6 residue 6 GLN Chi-restraints excluded: chain A6 residue 8 GLN Chi-restraints excluded: chain A9 residue 6 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN I 8 GLN L 8 GLN Q 8 GLN S 6 GLN 0 8 GLN 4 8 GLN x 6 GLN z 6 GLN AG 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.050277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.042555 restraints weight = 18112.059| |-----------------------------------------------------------------------------| r_work (start): 0.2426 rms_B_bonded: 2.46 r_work: 0.2287 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2164 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9279 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.102 0.471 7252 Z= 4.049 Angle : 3.576 26.468 9464 Z= 1.865 Chirality : 0.244 0.593 518 Planarity : 0.021 0.105 1134 Dihedral : 26.210 87.486 914 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 26.19 % Favored : 73.57 % Rotamer: Outliers : 9.46 % Allowed : 14.29 % Favored : 76.25 % Cbeta Deviations : 8.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 1.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.55 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.99 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.068 0.012 TYR g 7 PHE 0.092 0.013 PHE K 3 Details of bonding type rmsd covalent geometry : bond 0.10237 ( 7154) covalent geometry : angle 3.57601 ( 9464) Misc. bond : bond 0.00809 ( 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 145 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 0.242 Fit side-chains REVERT: E 8 GLN cc_start: 0.8746 (mt0) cc_final: 0.7470 (tm-30) REVERT: J 8 GLN cc_start: 0.9022 (mt0) cc_final: 0.7575 (tm-30) REVERT: K 6 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8251 (tm130) REVERT: R 6 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.7940 (tm130) REVERT: U 8 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: Y 8 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: 1 6 GLN cc_start: 0.8700 (tm-30) cc_final: 0.7928 (tm130) REVERT: 5 8 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: 9 8 GLN cc_start: 0.9039 (tt0) cc_final: 0.8272 (tm-30) REVERT: c 8 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7361 (tm-30) REVERT: j 8 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7640 (tm-30) REVERT: m 6 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: q 8 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: r 6 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8473 (tm130) REVERT: u 8 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: x 8 GLN cc_start: 0.9067 (mt0) cc_final: 0.7673 (tm-30) REVERT: AB 8 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: AE 8 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: AF 6 GLN cc_start: 0.9277 (tt0) cc_final: 0.7820 (tm130) REVERT: AH 6 GLN cc_start: 0.8613 (tm-30) cc_final: 0.7821 (tm130) REVERT: AI 8 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8472 (tm-30) REVERT: AK 8 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: AL 8 GLN cc_start: 0.8762 (mt0) cc_final: 0.7390 (tm-30) REVERT: AP 8 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8943 (tm-30) REVERT: AR 8 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8488 (tp-100) REVERT: AS 8 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: AY 2 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.9153 (t80) REVERT: AY 8 GLN cc_start: 0.8128 (mt0) cc_final: 0.7753 (mt0) REVERT: AZ 8 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: A3 8 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8596 (tm-30) REVERT: A6 8 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: A9 6 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7917 (tm-30) outliers start: 49 outliers final: 21 residues processed: 106 average time/residue: 0.9251 time to fit residues: 100.9174 Evaluate side-chains 140 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 96 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain Y residue 8 GLN Chi-restraints excluded: chain 2 residue 6 GLN Chi-restraints excluded: chain 4 residue 2 PHE Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 6 residue 6 GLN Chi-restraints excluded: chain c residue 8 GLN Chi-restraints excluded: chain d residue 6 GLN Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain j residue 6 GLN Chi-restraints excluded: chain j residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain p residue 2 PHE Chi-restraints excluded: chain q residue 5 PRO Chi-restraints excluded: chain q residue 8 GLN Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain u residue 8 GLN Chi-restraints excluded: chain AB residue 8 GLN Chi-restraints excluded: chain AD residue 2 PHE Chi-restraints excluded: chain AE residue 8 GLN Chi-restraints excluded: chain AI residue 8 GLN Chi-restraints excluded: chain AK residue 8 GLN Chi-restraints excluded: chain AP residue 6 GLN Chi-restraints excluded: chain AP residue 8 GLN Chi-restraints excluded: chain AR residue 2 PHE Chi-restraints excluded: chain AR residue 8 GLN Chi-restraints excluded: chain AS residue 8 GLN Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AZ residue 8 GLN Chi-restraints excluded: chain A0 residue 6 GLN Chi-restraints excluded: chain A1 residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Chi-restraints excluded: chain A3 residue 8 GLN Chi-restraints excluded: chain A6 residue 6 GLN Chi-restraints excluded: chain A6 residue 8 GLN Chi-restraints excluded: chain A9 residue 6 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN I 8 GLN L 8 GLN P 8 GLN Q 8 GLN S 6 GLN 0 8 GLN 4 8 GLN x 6 GLN z 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.050245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.042504 restraints weight = 17991.064| |-----------------------------------------------------------------------------| r_work (start): 0.2426 rms_B_bonded: 2.46 r_work: 0.2287 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2163 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9278 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.102 0.470 7252 Z= 4.050 Angle : 3.577 26.410 9464 Z= 1.864 Chirality : 0.245 0.592 518 Planarity : 0.021 0.105 1134 Dihedral : 26.224 87.534 914 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 27.14 % Favored : 72.62 % Rotamer: Outliers : 9.07 % Allowed : 14.09 % Favored : 76.83 % Cbeta Deviations : 8.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 1.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.55 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.98 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.068 0.012 TYR g 7 PHE 0.093 0.013 PHE K 3 Details of bonding type rmsd covalent geometry : bond 0.10239 ( 7154) covalent geometry : angle 3.57708 ( 9464) Misc. bond : bond 0.00824 ( 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 144 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 97 time to evaluate : 0.265 Fit side-chains REVERT: E 8 GLN cc_start: 0.8742 (mt0) cc_final: 0.7453 (tm-30) REVERT: J 8 GLN cc_start: 0.9018 (mt0) cc_final: 0.7566 (tm-30) REVERT: K 6 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8256 (tm130) REVERT: R 6 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.7925 (tm130) REVERT: U 8 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: Y 8 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.7711 (tm130) REVERT: 1 6 GLN cc_start: 0.8700 (tm-30) cc_final: 0.7951 (tm130) REVERT: 5 8 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: 9 8 GLN cc_start: 0.9031 (tt0) cc_final: 0.8264 (tm-30) REVERT: c 8 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: j 8 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: m 6 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: q 8 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: r 6 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8474 (tm130) REVERT: u 8 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: x 8 GLN cc_start: 0.9075 (mt0) cc_final: 0.7691 (tm-30) REVERT: AB 8 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: AE 8 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: AF 6 GLN cc_start: 0.9276 (tt0) cc_final: 0.7820 (tm130) REVERT: AH 6 GLN cc_start: 0.8608 (tm-30) cc_final: 0.7803 (tm130) REVERT: AK 8 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: AL 8 GLN cc_start: 0.8769 (mt0) cc_final: 0.7395 (tm-30) REVERT: AS 8 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: AY 2 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.9161 (t80) REVERT: AY 8 GLN cc_start: 0.8142 (mt0) cc_final: 0.7780 (mt0) REVERT: AZ 8 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: A3 8 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8571 (tm-30) REVERT: A6 8 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: A9 6 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7888 (tm-30) outliers start: 47 outliers final: 21 residues processed: 107 average time/residue: 0.9577 time to fit residues: 105.5321 Evaluate side-chains 138 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain Y residue 8 GLN Chi-restraints excluded: chain 2 residue 6 GLN Chi-restraints excluded: chain 4 residue 2 PHE Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 6 residue 6 GLN Chi-restraints excluded: chain c residue 8 GLN Chi-restraints excluded: chain d residue 6 GLN Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain j residue 6 GLN Chi-restraints excluded: chain j residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain p residue 2 PHE Chi-restraints excluded: chain q residue 5 PRO Chi-restraints excluded: chain q residue 8 GLN Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain u residue 8 GLN Chi-restraints excluded: chain AB residue 8 GLN Chi-restraints excluded: chain AD residue 2 PHE Chi-restraints excluded: chain AE residue 8 GLN Chi-restraints excluded: chain AK residue 8 GLN Chi-restraints excluded: chain AP residue 6 GLN Chi-restraints excluded: chain AR residue 2 PHE Chi-restraints excluded: chain AS residue 8 GLN Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AZ residue 8 GLN Chi-restraints excluded: chain A0 residue 6 GLN Chi-restraints excluded: chain A1 residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Chi-restraints excluded: chain A3 residue 8 GLN Chi-restraints excluded: chain A6 residue 6 GLN Chi-restraints excluded: chain A6 residue 8 GLN Chi-restraints excluded: chain A9 residue 6 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN I 8 GLN L 8 GLN P 8 GLN Q 8 GLN S 6 GLN 0 8 GLN 4 8 GLN x 6 GLN z 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.050232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.042481 restraints weight = 18271.363| |-----------------------------------------------------------------------------| r_work (start): 0.2423 rms_B_bonded: 2.47 r_work: 0.2285 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2161 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9279 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.102 0.469 7252 Z= 4.052 Angle : 3.580 26.439 9464 Z= 1.866 Chirality : 0.244 0.591 518 Planarity : 0.021 0.105 1134 Dihedral : 26.232 87.480 914 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 26.43 % Favored : 73.33 % Rotamer: Outliers : 8.49 % Allowed : 14.48 % Favored : 77.03 % Cbeta Deviations : 8.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 1.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.57 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.00 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.068 0.012 TYR g 7 PHE 0.093 0.013 PHE K 3 Details of bonding type rmsd covalent geometry : bond 0.10247 ( 7154) covalent geometry : angle 3.58018 ( 9464) Misc. bond : bond 0.00808 ( 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 140 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 96 time to evaluate : 0.251 Fit side-chains REVERT: E 8 GLN cc_start: 0.8750 (mt0) cc_final: 0.7466 (tm-30) REVERT: J 8 GLN cc_start: 0.9022 (mt0) cc_final: 0.7580 (tm-30) REVERT: K 6 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8262 (tm130) REVERT: R 6 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.7933 (tm130) REVERT: U 8 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: Y 8 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: 1 6 GLN cc_start: 0.8704 (tm-30) cc_final: 0.7956 (tm130) REVERT: 5 8 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: 9 8 GLN cc_start: 0.9041 (tt0) cc_final: 0.8267 (tm-30) REVERT: c 8 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: j 8 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: m 6 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: q 8 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: r 6 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8472 (tm130) REVERT: u 8 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: x 8 GLN cc_start: 0.9076 (mt0) cc_final: 0.7693 (tm-30) REVERT: AB 8 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8396 (tm-30) REVERT: AE 8 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: AF 6 GLN cc_start: 0.9280 (tt0) cc_final: 0.7825 (tm130) REVERT: AH 6 GLN cc_start: 0.8623 (tm-30) cc_final: 0.7741 (tm-30) REVERT: AK 8 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: AL 8 GLN cc_start: 0.8773 (mt0) cc_final: 0.7400 (tm-30) REVERT: AR 8 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8507 (tp-100) REVERT: AS 8 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: AY 2 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.9152 (t80) REVERT: AZ 8 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: A3 8 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8589 (tm-30) REVERT: A6 8 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: A9 6 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7910 (tm-30) outliers start: 44 outliers final: 21 residues processed: 105 average time/residue: 0.9091 time to fit residues: 98.3213 Evaluate side-chains 138 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain Y residue 8 GLN Chi-restraints excluded: chain 2 residue 6 GLN Chi-restraints excluded: chain 4 residue 2 PHE Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 6 residue 6 GLN Chi-restraints excluded: chain c residue 8 GLN Chi-restraints excluded: chain d residue 6 GLN Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain j residue 6 GLN Chi-restraints excluded: chain j residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain p residue 2 PHE Chi-restraints excluded: chain q residue 5 PRO Chi-restraints excluded: chain q residue 8 GLN Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain u residue 8 GLN Chi-restraints excluded: chain AB residue 8 GLN Chi-restraints excluded: chain AD residue 2 PHE Chi-restraints excluded: chain AE residue 8 GLN Chi-restraints excluded: chain AK residue 8 GLN Chi-restraints excluded: chain AP residue 6 GLN Chi-restraints excluded: chain AR residue 2 PHE Chi-restraints excluded: chain AR residue 8 GLN Chi-restraints excluded: chain AS residue 8 GLN Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AZ residue 8 GLN Chi-restraints excluded: chain A0 residue 6 GLN Chi-restraints excluded: chain A1 residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Chi-restraints excluded: chain A3 residue 8 GLN Chi-restraints excluded: chain A6 residue 6 GLN Chi-restraints excluded: chain A6 residue 8 GLN Chi-restraints excluded: chain A9 residue 6 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN I 8 GLN L 8 GLN P 8 GLN Q 8 GLN S 6 GLN 0 8 GLN 4 8 GLN x 6 GLN z 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.050213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.042498 restraints weight = 18246.617| |-----------------------------------------------------------------------------| r_work (start): 0.2425 rms_B_bonded: 2.46 r_work: 0.2286 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2162 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9279 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.102 0.471 7252 Z= 4.051 Angle : 3.580 26.436 9464 Z= 1.866 Chirality : 0.245 0.591 518 Planarity : 0.021 0.105 1134 Dihedral : 26.233 87.499 914 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 26.67 % Favored : 73.10 % Rotamer: Outliers : 8.69 % Allowed : 14.09 % Favored : 77.22 % Cbeta Deviations : 8.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 1.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.57 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.00 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.068 0.012 TYR g 7 PHE 0.093 0.013 PHE K 3 Details of bonding type rmsd covalent geometry : bond 0.10243 ( 7154) covalent geometry : angle 3.58003 ( 9464) Misc. bond : bond 0.00815 ( 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 143 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 98 time to evaluate : 0.223 Fit side-chains REVERT: E 8 GLN cc_start: 0.8749 (mt0) cc_final: 0.7450 (tm-30) REVERT: J 8 GLN cc_start: 0.9025 (mt0) cc_final: 0.7585 (tm-30) REVERT: K 6 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8258 (tm130) REVERT: R 6 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.7935 (tm130) REVERT: U 8 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: Y 8 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.7719 (tm130) REVERT: 1 6 GLN cc_start: 0.8710 (tm-30) cc_final: 0.7961 (tm130) REVERT: 5 8 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: 9 8 GLN cc_start: 0.9041 (tt0) cc_final: 0.8275 (tm-30) REVERT: c 8 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: j 8 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: m 6 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: q 8 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: r 6 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8474 (tm130) REVERT: u 8 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: x 8 GLN cc_start: 0.9076 (mt0) cc_final: 0.7691 (tm-30) REVERT: AB 8 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8373 (tm-30) REVERT: AE 8 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: AF 6 GLN cc_start: 0.9278 (tt0) cc_final: 0.7821 (tm130) REVERT: AH 6 GLN cc_start: 0.8632 (tm-30) cc_final: 0.7827 (tm130) REVERT: AK 8 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: AL 8 GLN cc_start: 0.8775 (mt0) cc_final: 0.7440 (tm-30) REVERT: AS 8 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: AY 2 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.9157 (t80) REVERT: AZ 8 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: A3 8 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8582 (tm-30) REVERT: A6 8 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: A9 6 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7911 (tm-30) outliers start: 45 outliers final: 20 residues processed: 107 average time/residue: 0.9324 time to fit residues: 102.7263 Evaluate side-chains 138 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain Y residue 8 GLN Chi-restraints excluded: chain 4 residue 2 PHE Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 6 residue 6 GLN Chi-restraints excluded: chain c residue 8 GLN Chi-restraints excluded: chain d residue 6 GLN Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain j residue 6 GLN Chi-restraints excluded: chain j residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain p residue 2 PHE Chi-restraints excluded: chain q residue 5 PRO Chi-restraints excluded: chain q residue 8 GLN Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain u residue 8 GLN Chi-restraints excluded: chain AB residue 8 GLN Chi-restraints excluded: chain AD residue 2 PHE Chi-restraints excluded: chain AE residue 8 GLN Chi-restraints excluded: chain AK residue 8 GLN Chi-restraints excluded: chain AP residue 6 GLN Chi-restraints excluded: chain AR residue 2 PHE Chi-restraints excluded: chain AS residue 8 GLN Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AZ residue 8 GLN Chi-restraints excluded: chain A0 residue 6 GLN Chi-restraints excluded: chain A1 residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Chi-restraints excluded: chain A3 residue 8 GLN Chi-restraints excluded: chain A6 residue 6 GLN Chi-restraints excluded: chain A6 residue 8 GLN Chi-restraints excluded: chain A9 residue 6 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN I 8 GLN L 8 GLN P 8 GLN Q 8 GLN S 6 GLN 0 8 GLN 4 8 GLN s 8 GLN x 6 GLN z 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.050223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.042532 restraints weight = 17895.186| |-----------------------------------------------------------------------------| r_work (start): 0.2426 rms_B_bonded: 2.44 r_work: 0.2287 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2163 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9278 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.102 0.471 7252 Z= 4.052 Angle : 3.581 26.438 9464 Z= 1.866 Chirality : 0.245 0.590 518 Planarity : 0.021 0.105 1134 Dihedral : 26.234 87.498 914 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 26.43 % Favored : 73.33 % Rotamer: Outliers : 8.11 % Allowed : 14.48 % Favored : 77.41 % Cbeta Deviations : 8.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 1.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.58 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.01 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.068 0.012 TYR g 7 PHE 0.093 0.013 PHE K 3 Details of bonding type rmsd covalent geometry : bond 0.10247 ( 7154) covalent geometry : angle 3.58054 ( 9464) Misc. bond : bond 0.00817 ( 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 139 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 97 time to evaluate : 0.280 Fit side-chains REVERT: E 8 GLN cc_start: 0.8751 (mt0) cc_final: 0.7457 (tm-30) REVERT: J 8 GLN cc_start: 0.9018 (mt0) cc_final: 0.7581 (tm-30) REVERT: K 6 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8258 (tm130) REVERT: R 6 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.7934 (tm130) REVERT: U 8 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: Y 8 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: 1 6 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8013 (tm130) REVERT: 5 8 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: 9 8 GLN cc_start: 0.9031 (tt0) cc_final: 0.8261 (tm-30) REVERT: c 8 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: j 8 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: m 6 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: q 8 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: r 6 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8474 (tm130) REVERT: u 8 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: x 8 GLN cc_start: 0.9071 (mt0) cc_final: 0.7689 (tm-30) REVERT: AB 8 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8375 (tm-30) REVERT: AE 8 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: AF 6 GLN cc_start: 0.9279 (tt0) cc_final: 0.7828 (tm130) REVERT: AH 6 GLN cc_start: 0.8631 (tm-30) cc_final: 0.7745 (tm-30) REVERT: AI 8 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: AK 8 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: AL 8 GLN cc_start: 0.8774 (mt0) cc_final: 0.7438 (tm-30) REVERT: AS 8 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: AY 2 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.9153 (t80) REVERT: AZ 8 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: A3 8 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8581 (tm-30) REVERT: A6 8 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: A9 6 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7919 (tm-30) outliers start: 42 outliers final: 21 residues processed: 106 average time/residue: 0.9802 time to fit residues: 106.9264 Evaluate side-chains 139 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 97 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain W residue 2 PHE Chi-restraints excluded: chain Y residue 8 GLN Chi-restraints excluded: chain 4 residue 2 PHE Chi-restraints excluded: chain 5 residue 8 GLN Chi-restraints excluded: chain 6 residue 6 GLN Chi-restraints excluded: chain c residue 8 GLN Chi-restraints excluded: chain d residue 6 GLN Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain g residue 6 GLN Chi-restraints excluded: chain j residue 6 GLN Chi-restraints excluded: chain j residue 8 GLN Chi-restraints excluded: chain k residue 6 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain p residue 2 PHE Chi-restraints excluded: chain q residue 5 PRO Chi-restraints excluded: chain q residue 8 GLN Chi-restraints excluded: chain r residue 6 GLN Chi-restraints excluded: chain u residue 8 GLN Chi-restraints excluded: chain AB residue 8 GLN Chi-restraints excluded: chain AD residue 2 PHE Chi-restraints excluded: chain AE residue 8 GLN Chi-restraints excluded: chain AI residue 8 GLN Chi-restraints excluded: chain AK residue 8 GLN Chi-restraints excluded: chain AP residue 6 GLN Chi-restraints excluded: chain AR residue 2 PHE Chi-restraints excluded: chain AS residue 8 GLN Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AZ residue 8 GLN Chi-restraints excluded: chain A0 residue 6 GLN Chi-restraints excluded: chain A1 residue 6 GLN Chi-restraints excluded: chain A3 residue 6 GLN Chi-restraints excluded: chain A3 residue 8 GLN Chi-restraints excluded: chain A6 residue 6 GLN Chi-restraints excluded: chain A6 residue 8 GLN Chi-restraints excluded: chain A9 residue 6 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN I 8 GLN L 8 GLN P 8 GLN Q 8 GLN S 6 GLN 0 8 GLN 4 8 GLN ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 6 GLN z 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.050208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.042478 restraints weight = 18151.625| |-----------------------------------------------------------------------------| r_work (start): 0.2425 rms_B_bonded: 2.46 r_work: 0.2286 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2163 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9279 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.102 0.471 7252 Z= 4.052 Angle : 3.581 26.436 9464 Z= 1.866 Chirality : 0.245 0.589 518 Planarity : 0.021 0.106 1134 Dihedral : 26.233 87.492 914 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 26.43 % Favored : 73.33 % Rotamer: Outliers : 8.11 % Allowed : 14.86 % Favored : 77.03 % Cbeta Deviations : 8.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 1.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.58 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.01 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.068 0.012 TYR g 7 PHE 0.094 0.013 PHE K 3 Details of bonding type rmsd covalent geometry : bond 0.10245 ( 7154) covalent geometry : angle 3.58079 ( 9464) Misc. bond : bond 0.00816 ( 98) =============================================================================== Job complete usr+sys time: 2281.29 seconds wall clock time: 39 minutes 25.74 seconds (2365.74 seconds total)