Starting phenix.real_space_refine on Mon Sep 23 18:36:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/09_2024/7uuq_26800.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/09_2024/7uuq_26800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/09_2024/7uuq_26800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/09_2024/7uuq_26800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/09_2024/7uuq_26800.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/09_2024/7uuq_26800.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 sd= 0.029 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 3640 2.51 5 N 364 2.21 5 O 756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4760 Number of models: 1 Model: "" Number of chains: 98 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 A 1 " pdbres="TYR A 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 B 1 " pdbres="TYR B 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9 C 1 " pdbres="TYR C 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 D 1 " pdbres="TYR D 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9 E 1 " pdbres="TYR E 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 F 1 " pdbres="TYR F 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 G 1 " pdbres="TYR G 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 H 1 " pdbres="TYR H 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 I 1 " pdbres="TYR I 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9 J 1 " pdbres="TYR J 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 K 1 " pdbres="TYR K 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9 L 1 " pdbres="TYR L 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 M 1 " pdbres="TYR M 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 N 1 " pdbres="TYR N 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 O 1 " pdbres="TYR O 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 P 1 " pdbres="TYR P 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9 Q 1 " pdbres="TYR Q 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 R 1 " pdbres="TYR R 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9 S 1 " pdbres="TYR S 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 T 1 " pdbres="TYR T 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 U 1 " pdbres="TYR U 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 V 1 " pdbres="TYR V 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 W 1 " pdbres="TYR W 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9 X 1 " pdbres="TYR X 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 Y 1 " pdbres="TYR Y 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9 Z 1 " pdbres="TYR Z 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 0 1 " pdbres="TYR 0 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 1 1 " pdbres="TYR 1 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 2 1 " pdbres="TYR 2 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 3 1 " pdbres="TYR 3 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9 4 1 " pdbres="TYR 4 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 5 1 " pdbres="TYR 5 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9 6 1 " pdbres="TYR 6 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 7 1 " pdbres="TYR 7 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 8 1 " pdbres="TYR 8 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 9 1 " pdbres="TYR 9 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 a 1 " pdbres="TYR a 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9 b 1 " pdbres="TYR b 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 c 1 " pdbres="TYR c 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9 d 1 " pdbres="TYR d 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 e 1 " pdbres="TYR e 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 f 1 " pdbres="TYR f 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 g 1 " pdbres="TYR g 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 h 1 " pdbres="TYR h 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9 i 1 " pdbres="TYR i 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 j 1 " pdbres="TYR j 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9 k 1 " pdbres="TYR k 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 l 1 " pdbres="TYR l 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 m 1 " pdbres="TYR m 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 n 1 " pdbres="TYR n 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 o 1 " pdbres="TYR o 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9 p 1 " pdbres="TYR p 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 q 1 " pdbres="TYR q 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9 r 1 " pdbres="TYR r 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 s 1 " pdbres="TYR s 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 t 1 " pdbres="TYR t 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 u 1 " pdbres="TYR u 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 v 1 " pdbres="TYR v 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9 w 1 " pdbres="TYR w 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9 x 1 " pdbres="TYR x 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9 y 1 " pdbres="TYR y 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9 z 1 " pdbres="TYR z 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9AA 1 " pdbres="TYRAA 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9AB 1 " pdbres="TYRAB 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AC" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9AC 1 " pdbres="TYRAC 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AD" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9AD 1 " pdbres="TYRAD 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AE" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9AE 1 " pdbres="TYRAE 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AF" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9AF 1 " pdbres="TYRAF 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AG" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9AG 1 " pdbres="TYRAG 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AH" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9AH 1 " pdbres="TYRAH 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AI" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9AI 1 " pdbres="TYRAI 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AJ" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9AJ 1 " pdbres="TYRAJ 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AK" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9AK 1 " pdbres="TYRAK 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AL" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9AL 1 " pdbres="TYRAL 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9AM 1 " pdbres="TYRAM 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AN" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9AN 1 " pdbres="TYRAN 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AO" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9AO 1 " pdbres="TYRAO 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AP" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9AP 1 " pdbres="TYRAP 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AQ" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9AQ 1 " pdbres="TYRAQ 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AR" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9AR 1 " pdbres="TYRAR 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AS" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9AS 1 " pdbres="TYRAS 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AT" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9AT 1 " pdbres="TYRAT 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AU" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9AU 1 " pdbres="TYRAU 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AV" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9AV 1 " pdbres="TYRAV 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AW" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9AW 1 " pdbres="TYRAW 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AX" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9AX 1 " pdbres="TYRAX 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AY" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9AY 1 " pdbres="TYRAY 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AZ" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9AZ 1 " pdbres="TYRAZ 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A0" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9A0 1 " pdbres="TYRA0 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A1" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9A1 1 " pdbres="TYRA1 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A2" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9A2 1 " pdbres="TYRA2 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A3" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9A3 1 " pdbres="TYRA3 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A4" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9A4 1 " pdbres="TYRA4 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A5" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {'OG9': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OG9A5 1 " pdbres="TYRA5 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A6" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'OG9': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 3, None: 1} Not linked: pdbres="OG9A6 1 " pdbres="TYRA6 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A7" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'OG9': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="OG9A7 1 " pdbres="TYRA7 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A8" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9A8 1 " pdbres="TYRA8 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A9" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'OG9': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="OG9A9 1 " pdbres="TYRA9 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.43, per 1000 atoms: 0.72 Number of scatterers: 4760 At special positions: 0 Unit cell: (61.56, 57.24, 86.4, 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 756 8.00 N 364 7.00 C 3640 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: 1.24 Conformation dependent library (CDL) restraints added in 196.3 milliseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 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: 0.72 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.27: 462 1.27 - 1.34: 238 1.34 - 1.41: 1982 1.41 - 1.48: 1252 1.48 - 1.55: 1190 Bond restraints: 5124 Sorted by residual: bond pdb=" C16 OG9AO 1 " pdb=" C17 OG9AO 1 " ideal model delta sigma weight residual 1.423 1.353 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C16 OG9 t 1 " pdb=" C17 OG9 t 1 " ideal model delta sigma weight residual 1.423 1.353 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C16 OG9A2 1 " pdb=" C17 OG9A2 1 " ideal model delta sigma weight residual 1.423 1.353 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C16 OG9 8 1 " pdb=" C17 OG9 8 1 " ideal model delta sigma weight residual 1.423 1.353 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C16 OG9 G 1 " pdb=" C17 OG9 G 1 " ideal model delta sigma weight residual 1.423 1.353 0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 5119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 6448 2.81 - 5.63: 589 5.63 - 8.44: 47 8.44 - 11.26: 28 11.26 - 14.07: 14 Bond angle restraints: 7126 Sorted by residual: angle pdb=" C OG9AA 1 " pdb=" CA OG9AA 1 " pdb=" C05 OG9AA 1 " ideal model delta sigma weight residual 114.71 100.64 14.07 3.00e+00 1.11e-01 2.20e+01 angle pdb=" C OG9AO 1 " pdb=" CA OG9AO 1 " pdb=" C05 OG9AO 1 " ideal model delta sigma weight residual 114.71 100.66 14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" C OG9A2 1 " pdb=" CA OG9A2 1 " pdb=" C05 OG9A2 1 " ideal model delta sigma weight residual 114.71 100.66 14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" C OG9 N 1 " pdb=" CA OG9 N 1 " pdb=" C05 OG9 N 1 " ideal model delta sigma weight residual 114.71 100.67 14.04 3.00e+00 1.11e-01 2.19e+01 angle pdb=" C OG9A9 1 " pdb=" CA OG9A9 1 " pdb=" C05 OG9A9 1 " ideal model delta sigma weight residual 114.71 100.67 14.04 3.00e+00 1.11e-01 2.19e+01 ... (remaining 7121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 1652 17.03 - 34.06: 266 34.06 - 51.09: 28 51.09 - 68.11: 28 68.11 - 85.14: 14 Dihedral angle restraints: 1988 sinusoidal: 896 harmonic: 1092 Sorted by residual: dihedral pdb=" CA SER Q 3 " pdb=" C SER Q 3 " pdb=" N PRO Q 4 " pdb=" CA PRO Q 4 " ideal model delta harmonic sigma weight residual 180.00 165.82 14.18 0 5.00e+00 4.00e-02 8.05e+00 dihedral pdb=" CA SERAR 3 " pdb=" C SERAR 3 " pdb=" N PROAR 4 " pdb=" CA PROAR 4 " ideal model delta harmonic sigma weight residual 180.00 165.85 14.15 0 5.00e+00 4.00e-02 8.01e+00 dihedral pdb=" CA SER X 3 " pdb=" C SER X 3 " pdb=" N PRO X 4 " pdb=" CA PRO X 4 " ideal model delta harmonic sigma weight residual 180.00 165.86 14.14 0 5.00e+00 4.00e-02 8.00e+00 ... (remaining 1985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 238 0.038 - 0.076: 125 0.076 - 0.115: 43 0.115 - 0.153: 0 0.153 - 0.191: 14 Chirality restraints: 420 Sorted by residual: chirality pdb=" CA TYR o 2 " pdb=" N TYR o 2 " pdb=" C TYR o 2 " pdb=" CB TYR o 2 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA TYR a 2 " pdb=" N TYR a 2 " pdb=" C TYR a 2 " pdb=" CB TYR a 2 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA TYR W 2 " pdb=" N TYR W 2 " pdb=" C TYR W 2 " pdb=" CB TYR W 2 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 417 not shown) Planarity restraints: 532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SERAQ 3 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C SERAQ 3 " -0.050 2.00e-02 2.50e+03 pdb=" O SERAQ 3 " 0.019 2.00e-02 2.50e+03 pdb=" N PROAQ 4 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SERAC 3 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C SERAC 3 " -0.050 2.00e-02 2.50e+03 pdb=" O SERAC 3 " 0.019 2.00e-02 2.50e+03 pdb=" N PROAC 4 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SERAJ 3 " 0.015 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C SERAJ 3 " -0.050 2.00e-02 2.50e+03 pdb=" O SERAJ 3 " 0.019 2.00e-02 2.50e+03 pdb=" N PROAJ 4 " 0.017 2.00e-02 2.50e+03 ... (remaining 529 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 13 2.47 - 3.08: 3847 3.08 - 3.69: 5995 3.69 - 4.29: 15041 4.29 - 4.90: 19292 Nonbonded interactions: 44188 Sorted by model distance: nonbonded pdb=" O OG9 f 1 " pdb=" OH TYR k 2 " model vdw 1.865 3.040 nonbonded pdb=" O OG9 G 1 " pdb=" OH TYR y 2 " model vdw 1.865 3.040 nonbonded pdb=" O OG9AV 1 " pdb=" OH TYRA0 2 " model vdw 1.865 3.040 nonbonded pdb=" O OG9 8 1 " pdb=" OH TYR d 2 " model vdw 1.865 3.040 nonbonded pdb=" O OG9AH 1 " pdb=" OH TYRAM 2 " model vdw 1.865 3.040 ... (remaining 44183 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '7' selection = chain '8' selection = chain 'A1' selection = chain 'A2' selection = chain 'A8' selection = chain 'A9' selection = chain 'AA' selection = chain 'AG' selection = chain 'AH' selection = chain 'AN' selection = chain 'AO' selection = chain 'AU' selection = chain 'AV' selection = chain 'F' selection = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'T' selection = chain 'U' selection = chain 'e' selection = chain 'f' selection = chain 'l' selection = chain 'm' selection = chain 's' selection = chain 't' selection = chain 'z' } ncs_group { reference = chain '2' selection = chain '3' selection = chain '5' selection = chain '9' selection = chain 'A' selection = chain 'A3' selection = chain 'A4' selection = chain 'A6' selection = chain 'AB' selection = chain 'AC' selection = chain 'AE' selection = chain 'AI' selection = chain 'AJ' selection = chain 'AL' selection = chain 'AP' selection = chain 'AQ' selection = chain 'AS' selection = chain 'AW' selection = chain 'AX' selection = chain 'AZ' selection = chain 'B' selection = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'u' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain '4' selection = chain 'A5' selection = chain 'AD' selection = chain 'AK' selection = chain 'AR' selection = chain 'AY' selection = chain 'C' selection = chain 'J' selection = chain 'Q' selection = chain 'X' selection = chain 'b' selection = chain 'i' selection = chain 'p' selection = chain 'w' } ncs_group { reference = chain '6' selection = chain 'A0' selection = chain 'A7' selection = chain 'AF' selection = chain 'AM' selection = chain 'AT' selection = chain 'E' selection = chain 'L' selection = chain 'S' selection = chain 'Z' selection = chain 'd' selection = chain 'k' selection = chain 'r' selection = chain 'y' } 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.070 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 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 : 0.018 0.070 5124 Z= 0.983 Angle : 1.823 14.070 7126 Z= 0.791 Chirality : 0.058 0.191 420 Planarity : 0.012 0.048 532 Dihedral : 18.293 85.142 1260 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.31 (0.28), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.09 (0.22), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.033 0.004 TYR P 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.479 Fit side-chains REVERT: K 2 TYR cc_start: 0.8945 (m-80) cc_final: 0.8735 (m-80) REVERT: R 2 TYR cc_start: 0.9101 (m-80) cc_final: 0.8887 (m-80) REVERT: q 2 TYR cc_start: 0.9198 (m-80) cc_final: 0.8863 (m-80) REVERT: x 2 TYR cc_start: 0.9179 (m-80) cc_final: 0.8977 (m-80) REVERT: A6 2 TYR cc_start: 0.9026 (m-80) cc_final: 0.8754 (m-80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0883 time to fit residues: 12.1230 Evaluate side-chains 55 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.117 0.608 5124 Z= 6.550 Angle : 4.388 40.365 7126 Z= 1.779 Chirality : 0.233 0.516 420 Planarity : 0.022 0.084 532 Dihedral : 38.658 89.542 658 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 48.25 Ramachandran Plot: Outliers : 23.21 % Allowed : 44.05 % Favored : 32.74 % Rotamer: Outliers : 7.69 % Allowed : 6.32 % Favored : 85.99 % Cbeta Deviations : 1.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.03 (0.47), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.64 (0.36), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.075 0.016 TYR B 2 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 10 time to evaluate : 0.447 Fit side-chains outliers start: 28 outliers final: 21 residues processed: 37 average time/residue: 0.0641 time to fit residues: 4.4583 Evaluate side-chains 31 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 10 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain I residue 3 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain 2 residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain n residue 3 SER Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain q residue 3 SER Chi-restraints excluded: chain x residue 3 SER Chi-restraints excluded: chain AL residue 5 THR Chi-restraints excluded: chain AS residue 3 SER Chi-restraints excluded: chain AS residue 5 THR Chi-restraints excluded: chain AW residue 3 SER Chi-restraints excluded: chain A4 residue 3 SER Chi-restraints excluded: chain A6 residue 3 SER 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.117 0.612 5124 Z= 6.555 Angle : 4.445 39.280 7126 Z= 1.797 Chirality : 0.231 0.503 420 Planarity : 0.024 0.083 532 Dihedral : 37.005 89.023 658 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 46.22 Ramachandran Plot: Outliers : 1.79 % Allowed : 68.45 % Favored : 29.76 % Rotamer: Outliers : 11.54 % Allowed : 8.79 % Favored : 79.67 % Cbeta Deviations : 2.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.26 (0.43), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.82 (0.33), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.074 0.015 TYR S 2 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 7 time to evaluate : 0.458 Fit side-chains outliers start: 42 outliers final: 32 residues processed: 48 average time/residue: 0.0650 time to fit residues: 5.6302 Evaluate side-chains 39 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 7 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain I residue 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain 2 residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain n residue 3 SER Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain q residue 3 SER Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain x residue 3 SER Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AK residue 5 THR Chi-restraints excluded: chain AL residue 3 SER Chi-restraints excluded: chain AL residue 5 THR Chi-restraints excluded: chain AS residue 3 SER Chi-restraints excluded: chain AS residue 5 THR Chi-restraints excluded: chain AW residue 3 SER Chi-restraints excluded: chain AZ residue 5 THR Chi-restraints excluded: chain A4 residue 3 SER Chi-restraints excluded: chain A6 residue 3 SER 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.117 0.601 5124 Z= 6.556 Angle : 4.425 39.814 7126 Z= 1.793 Chirality : 0.231 0.511 420 Planarity : 0.025 0.090 532 Dihedral : 37.011 89.759 658 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 45.25 Ramachandran Plot: Outliers : 2.38 % Allowed : 67.86 % Favored : 29.76 % Rotamer: Outliers : 13.19 % Allowed : 10.44 % Favored : 76.37 % Cbeta Deviations : 3.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.43 (0.43), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.95 (0.32), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.073 0.015 TYR S 2 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 7 time to evaluate : 0.470 Fit side-chains outliers start: 48 outliers final: 42 residues processed: 54 average time/residue: 0.0718 time to fit residues: 6.9340 Evaluate side-chains 48 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 6 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain I residue 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain 2 residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain n residue 3 SER Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain q residue 3 SER Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain u residue 6 SER Chi-restraints excluded: chain x residue 3 SER Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AK residue 5 THR Chi-restraints excluded: chain AL residue 3 SER Chi-restraints excluded: chain AL residue 5 THR Chi-restraints excluded: chain AS residue 3 SER Chi-restraints excluded: chain AS residue 5 THR Chi-restraints excluded: chain AW residue 3 SER Chi-restraints excluded: chain AY residue 5 THR Chi-restraints excluded: chain AZ residue 5 THR Chi-restraints excluded: chain A4 residue 3 SER Chi-restraints excluded: chain A5 residue 5 THR Chi-restraints excluded: chain A6 residue 3 SER 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.117 0.614 5124 Z= 6.554 Angle : 4.418 39.834 7126 Z= 1.790 Chirality : 0.230 0.519 420 Planarity : 0.025 0.092 532 Dihedral : 36.794 89.366 658 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 46.22 Ramachandran Plot: Outliers : 1.19 % Allowed : 67.86 % Favored : 30.95 % Rotamer: Outliers : 13.46 % Allowed : 11.54 % Favored : 75.00 % Cbeta Deviations : 3.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.49 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.99 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.071 0.015 TYR S 2 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 8 time to evaluate : 0.465 Fit side-chains outliers start: 49 outliers final: 43 residues processed: 57 average time/residue: 0.0657 time to fit residues: 6.6047 Evaluate side-chains 50 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 7 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain 2 residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain n residue 3 SER Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain q residue 3 SER Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain u residue 6 SER Chi-restraints excluded: chain x residue 3 SER Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AI residue 6 SER Chi-restraints excluded: chain AK residue 5 THR Chi-restraints excluded: chain AL residue 3 SER Chi-restraints excluded: chain AL residue 5 THR Chi-restraints excluded: chain AS residue 3 SER Chi-restraints excluded: chain AS residue 5 THR Chi-restraints excluded: chain AW residue 3 SER Chi-restraints excluded: chain AY residue 5 THR Chi-restraints excluded: chain AZ residue 5 THR Chi-restraints excluded: chain A0 residue 3 SER Chi-restraints excluded: chain A3 residue 6 SER Chi-restraints excluded: chain A4 residue 3 SER Chi-restraints excluded: chain A5 residue 5 THR Chi-restraints excluded: chain A6 residue 3 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.117 0.606 5124 Z= 6.552 Angle : 4.411 39.774 7126 Z= 1.787 Chirality : 0.231 0.518 420 Planarity : 0.025 0.093 532 Dihedral : 36.803 89.408 658 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 47.33 Ramachandran Plot: Outliers : 1.79 % Allowed : 67.26 % Favored : 30.95 % Rotamer: Outliers : 13.74 % Allowed : 12.91 % Favored : 73.35 % Cbeta Deviations : 3.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.53 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.02 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.071 0.015 TYR S 2 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 8 time to evaluate : 0.438 Fit side-chains REVERT: AP 6 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7375 (p) outliers start: 50 outliers final: 45 residues processed: 58 average time/residue: 0.0656 time to fit residues: 6.7252 Evaluate side-chains 53 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 7 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain I residue 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain 2 residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain n residue 3 SER Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain q residue 3 SER Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain u residue 6 SER Chi-restraints excluded: chain x residue 3 SER Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AK residue 5 THR Chi-restraints excluded: chain AL residue 3 SER Chi-restraints excluded: chain AL residue 5 THR Chi-restraints excluded: chain AP residue 6 SER Chi-restraints excluded: chain AS residue 3 SER Chi-restraints excluded: chain AS residue 5 THR Chi-restraints excluded: chain AW residue 3 SER Chi-restraints excluded: chain AY residue 5 THR Chi-restraints excluded: chain AZ residue 5 THR Chi-restraints excluded: chain A0 residue 3 SER Chi-restraints excluded: chain A3 residue 6 SER Chi-restraints excluded: chain A4 residue 3 SER Chi-restraints excluded: chain A5 residue 5 THR Chi-restraints excluded: chain A6 residue 3 SER 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.117 0.611 5124 Z= 6.549 Angle : 4.408 39.794 7126 Z= 1.785 Chirality : 0.231 0.521 420 Planarity : 0.025 0.093 532 Dihedral : 36.778 89.350 658 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 47.74 Ramachandran Plot: Outliers : 1.79 % Allowed : 67.26 % Favored : 30.95 % Rotamer: Outliers : 13.74 % Allowed : 13.46 % Favored : 72.80 % Cbeta Deviations : 2.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.53 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.02 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.071 0.015 TYR S 2 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 8 time to evaluate : 0.444 Fit side-chains outliers start: 50 outliers final: 48 residues processed: 58 average time/residue: 0.0668 time to fit residues: 6.8253 Evaluate side-chains 55 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 7 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain I residue 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain 2 residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain n residue 3 SER Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain q residue 3 SER Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain u residue 6 SER Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain x residue 3 SER Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AI residue 6 SER Chi-restraints excluded: chain AK residue 5 THR Chi-restraints excluded: chain AL residue 3 SER Chi-restraints excluded: chain AL residue 5 THR Chi-restraints excluded: chain AP residue 6 SER Chi-restraints excluded: chain AS residue 3 SER Chi-restraints excluded: chain AS residue 5 THR Chi-restraints excluded: chain AW residue 3 SER Chi-restraints excluded: chain AY residue 5 THR Chi-restraints excluded: chain AZ residue 5 THR Chi-restraints excluded: chain A0 residue 3 SER Chi-restraints excluded: chain A3 residue 6 SER Chi-restraints excluded: chain A4 residue 3 SER Chi-restraints excluded: chain A5 residue 5 THR Chi-restraints excluded: chain A6 residue 3 SER 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.117 0.610 5124 Z= 6.549 Angle : 4.410 39.779 7126 Z= 1.785 Chirality : 0.231 0.520 420 Planarity : 0.025 0.093 532 Dihedral : 36.763 89.359 658 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 46.20 Ramachandran Plot: Outliers : 1.79 % Allowed : 67.86 % Favored : 30.36 % Rotamer: Outliers : 14.01 % Allowed : 13.46 % Favored : 72.53 % Cbeta Deviations : 3.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.54 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.03 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.072 0.015 TYR S 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 7 time to evaluate : 0.423 Fit side-chains outliers start: 51 outliers final: 49 residues processed: 58 average time/residue: 0.0671 time to fit residues: 6.9370 Evaluate side-chains 54 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 5 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain I residue 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain 2 residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain 9 residue 3 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain n residue 3 SER Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain q residue 3 SER Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain u residue 6 SER Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain x residue 3 SER Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AI residue 6 SER Chi-restraints excluded: chain AK residue 5 THR Chi-restraints excluded: chain AL residue 3 SER Chi-restraints excluded: chain AL residue 5 THR Chi-restraints excluded: chain AP residue 6 SER Chi-restraints excluded: chain AS residue 3 SER Chi-restraints excluded: chain AS residue 5 THR Chi-restraints excluded: chain AW residue 3 SER Chi-restraints excluded: chain AY residue 5 THR Chi-restraints excluded: chain AZ residue 5 THR Chi-restraints excluded: chain A0 residue 3 SER Chi-restraints excluded: chain A3 residue 6 SER Chi-restraints excluded: chain A4 residue 3 SER Chi-restraints excluded: chain A5 residue 5 THR Chi-restraints excluded: chain A6 residue 3 SER 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.117 0.610 5124 Z= 6.552 Angle : 4.417 39.789 7126 Z= 1.789 Chirality : 0.230 0.520 420 Planarity : 0.025 0.093 532 Dihedral : 36.719 89.358 658 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 46.47 Ramachandran Plot: Outliers : 1.79 % Allowed : 67.86 % Favored : 30.36 % Rotamer: Outliers : 13.74 % Allowed : 14.29 % Favored : 71.98 % Cbeta Deviations : 2.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.54 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.03 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.071 0.015 TYR S 2 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 8 time to evaluate : 0.488 Fit side-chains outliers start: 50 outliers final: 48 residues processed: 58 average time/residue: 0.0665 time to fit residues: 6.8502 Evaluate side-chains 56 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 8 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain I residue 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain 2 residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain 9 residue 3 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain n residue 3 SER Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain q residue 3 SER Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain u residue 6 SER Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain x residue 3 SER Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AK residue 5 THR Chi-restraints excluded: chain AL residue 3 SER Chi-restraints excluded: chain AL residue 5 THR Chi-restraints excluded: chain AP residue 6 SER Chi-restraints excluded: chain AS residue 3 SER Chi-restraints excluded: chain AS residue 5 THR Chi-restraints excluded: chain AW residue 3 SER Chi-restraints excluded: chain AY residue 5 THR Chi-restraints excluded: chain AZ residue 5 THR Chi-restraints excluded: chain A0 residue 3 SER Chi-restraints excluded: chain A3 residue 6 SER Chi-restraints excluded: chain A4 residue 3 SER Chi-restraints excluded: chain A5 residue 5 THR Chi-restraints excluded: chain A6 residue 3 SER 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.117 0.612 5124 Z= 6.549 Angle : 4.429 39.780 7126 Z= 1.793 Chirality : 0.230 0.520 420 Planarity : 0.025 0.093 532 Dihedral : 36.688 89.398 658 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 46.49 Ramachandran Plot: Outliers : 2.38 % Allowed : 67.26 % Favored : 30.36 % Rotamer: Outliers : 13.19 % Allowed : 14.56 % Favored : 72.25 % Cbeta Deviations : 2.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.55 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.04 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.071 0.015 TYR S 2 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 7 time to evaluate : 0.464 Fit side-chains outliers start: 48 outliers final: 48 residues processed: 55 average time/residue: 0.0680 time to fit residues: 6.5703 Evaluate side-chains 55 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 7 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain I residue 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain 2 residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain 9 residue 3 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain n residue 3 SER Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain q residue 3 SER Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain u residue 6 SER Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain x residue 3 SER Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AK residue 5 THR Chi-restraints excluded: chain AL residue 3 SER Chi-restraints excluded: chain AL residue 5 THR Chi-restraints excluded: chain AP residue 6 SER Chi-restraints excluded: chain AS residue 3 SER Chi-restraints excluded: chain AS residue 5 THR Chi-restraints excluded: chain AW residue 3 SER Chi-restraints excluded: chain AY residue 5 THR Chi-restraints excluded: chain AZ residue 5 THR Chi-restraints excluded: chain A0 residue 3 SER Chi-restraints excluded: chain A3 residue 6 SER Chi-restraints excluded: chain A4 residue 3 SER Chi-restraints excluded: chain A5 residue 5 THR Chi-restraints excluded: chain A6 residue 3 SER 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.071438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.053139 restraints weight = 14462.729| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.45 r_work: 0.2601 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.117 0.611 5124 Z= 6.549 Angle : 4.425 39.767 7126 Z= 1.792 Chirality : 0.230 0.520 420 Planarity : 0.025 0.093 532 Dihedral : 36.695 89.403 658 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 46.48 Ramachandran Plot: Outliers : 2.38 % Allowed : 67.26 % Favored : 30.36 % Rotamer: Outliers : 13.19 % Allowed : 14.29 % Favored : 72.53 % Cbeta Deviations : 2.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.55 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.03 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.071 0.015 TYR S 2 =============================================================================== Job complete usr+sys time: 614.08 seconds wall clock time: 12 minutes 20.40 seconds (740.40 seconds total)