Starting phenix.real_space_refine on Sun Mar 10 20:11:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/03_2024/7uuq_26800_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/03_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_26800/03_2024/7uuq_26800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/03_2024/7uuq_26800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/03_2024/7uuq_26800_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/03_2024/7uuq_26800_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.41, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 2.46 Conformation dependent library (CDL) restraints added in 281.0 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: 0.56 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: 2.60 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: 97.31 - 103.97: 239 103.97 - 110.62: 889 110.62 - 117.28: 888 117.28 - 123.94: 4984 123.94 - 130.60: 126 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 - 0.077: 125 0.077 - 0.115: 43 0.115 - 0.153: 0 0.153 - 0.192: 14 Chirality restraints: 420 Sorted by residual: chirality pdb=" CA TYRAC 2 " pdb=" N TYRAC 2 " pdb=" C TYRAC 2 " pdb=" CB TYRAC 2 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.18e-01 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 ... (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: 5996 3.69 - 4.29: 15040 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 2.440 nonbonded pdb=" O OG9 G 1 " pdb=" OH TYR y 2 " model vdw 1.865 2.440 nonbonded pdb=" O OG9AV 1 " pdb=" OH TYRA0 2 " model vdw 1.865 2.440 nonbonded pdb=" O OG9 8 1 " pdb=" OH TYR d 2 " model vdw 1.865 2.440 nonbonded pdb=" O OG9AH 1 " pdb=" OH TYRAM 2 " model vdw 1.865 2.440 ... (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 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: 4.220 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: 6.830 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 15.400 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.110 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.990 ------------------------------------------------------------------------------- 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= 0.986 Angle : 1.823 14.070 7126 Z= 0.792 Chirality : 0.058 0.192 420 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 : 0.458 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: 0.0881 time to fit residues: 12.1047 Evaluate side-chains 55 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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: 0.8949 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.118 0.619 5124 Z= 6.603 Angle : 4.490 38.352 7126 Z= 1.847 Chirality : 0.234 0.520 420 Planarity : 0.022 0.083 532 Dihedral : 39.400 89.645 658 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 56.05 Ramachandran Plot: Outliers : 29.76 % Allowed : 41.67 % Favored : 28.57 % Rotamer: Outliers : 10.71 % Allowed : 10.16 % Favored : 79.12 % Cbeta Deviations : 1.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 6.12 % 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: -10.41 (0.46), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.93 (0.35), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.082 0.016 TYR P 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 48 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 9 time to evaluate : 0.457 Fit side-chains outliers start: 39 outliers final: 33 residues processed: 48 average time/residue: 0.0777 time to fit residues: 6.6848 Evaluate side-chains 41 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 8 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 3 residue 3 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain a residue 3 SER Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain g residue 3 SER 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 u residue 3 SER Chi-restraints excluded: chain x residue 3 SER Chi-restraints excluded: chain AC residue 3 SER Chi-restraints excluded: chain AI residue 3 SER Chi-restraints excluded: chain AL residue 5 THR Chi-restraints excluded: chain AQ residue 3 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 AZ residue 5 THR Chi-restraints excluded: chain A0 residue 3 SER Chi-restraints excluded: chain A3 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: 0.8947 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.118 0.612 5124 Z= 6.614 Angle : 4.536 38.362 7126 Z= 1.864 Chirality : 0.232 0.524 420 Planarity : 0.025 0.088 532 Dihedral : 37.560 89.065 658 Min Nonbonded Distance : 1.582 Molprobity Statistics. All-atom Clashscore : 54.60 Ramachandran Plot: Outliers : 4.17 % Allowed : 64.29 % Favored : 31.55 % Rotamer: Outliers : 19.23 % Allowed : 11.26 % Favored : 69.51 % Cbeta Deviations : 2.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.61 % 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: -10.76 (0.39), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.20 (0.30), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.072 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 75 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 5 time to evaluate : 0.745 Fit side-chains outliers start: 70 outliers final: 52 residues processed: 75 average time/residue: 0.0661 time to fit residues: 8.5814 Evaluate side-chains 57 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 5 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER 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 L residue 3 SER 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 3 residue 3 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain 6 residue 3 SER Chi-restraints excluded: chain 9 residue 3 SER Chi-restraints excluded: chain a residue 3 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain g residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain k residue 3 SER 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 r residue 3 SER Chi-restraints excluded: chain u residue 3 SER Chi-restraints excluded: chain x residue 3 SER Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain y residue 3 SER Chi-restraints excluded: chain AB residue 3 SER Chi-restraints excluded: chain AC residue 3 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AF residue 3 SER Chi-restraints excluded: chain AI residue 3 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 AM residue 3 SER Chi-restraints excluded: chain AQ residue 3 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 AZ residue 5 THR Chi-restraints excluded: chain A3 residue 3 SER Chi-restraints excluded: chain A4 residue 3 SER Chi-restraints excluded: chain A6 residue 3 SER Chi-restraints excluded: chain A7 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: 0.8946 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.118 0.612 5124 Z= 6.610 Angle : 4.549 38.663 7126 Z= 1.863 Chirality : 0.231 0.516 420 Planarity : 0.025 0.089 532 Dihedral : 37.704 89.811 658 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 56.00 Ramachandran Plot: Outliers : 3.57 % Allowed : 67.26 % Favored : 29.17 % Rotamer: Outliers : 20.60 % Allowed : 10.71 % Favored : 68.68 % Cbeta Deviations : 3.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.61 % 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: -10.85 (0.39), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.27 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.076 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 79 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 4 time to evaluate : 0.485 Fit side-chains outliers start: 75 outliers final: 65 residues processed: 79 average time/residue: 0.0681 time to fit residues: 9.1835 Evaluate side-chains 70 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 5 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER 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 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z 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 6 residue 3 SER Chi-restraints excluded: chain 9 residue 3 SER Chi-restraints excluded: chain a residue 3 SER Chi-restraints excluded: chain b residue 3 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain g residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain k residue 3 SER 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 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 y residue 3 SER Chi-restraints excluded: chain AB residue 3 SER Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AC residue 3 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AF residue 3 SER Chi-restraints excluded: chain AI residue 3 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 AM residue 3 SER Chi-restraints excluded: chain AQ residue 3 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 3 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 Chi-restraints excluded: chain A7 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: 0.8945 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.118 0.619 5124 Z= 6.611 Angle : 4.535 38.848 7126 Z= 1.861 Chirality : 0.232 0.520 420 Planarity : 0.025 0.089 532 Dihedral : 37.414 89.617 658 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 56.55 Ramachandran Plot: Outliers : 3.57 % Allowed : 66.07 % Favored : 30.36 % Rotamer: Outliers : 21.70 % Allowed : 11.26 % Favored : 67.03 % Cbeta Deviations : 3.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.61 % 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: -10.87 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.29 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.074 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 84 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 5 time to evaluate : 0.467 Fit side-chains outliers start: 79 outliers final: 66 residues processed: 84 average time/residue: 0.0631 time to fit residues: 9.1672 Evaluate side-chains 70 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 4 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 3 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 L residue 3 SER Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z 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 6 residue 3 SER Chi-restraints excluded: chain 9 residue 3 SER Chi-restraints excluded: chain a residue 3 SER Chi-restraints excluded: chain b residue 3 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain g residue 3 SER Chi-restraints excluded: chain i residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain k residue 3 SER 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 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 y residue 3 SER Chi-restraints excluded: chain AB residue 3 SER Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AC residue 3 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AF residue 3 SER Chi-restraints excluded: chain AI residue 3 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 AM residue 3 SER Chi-restraints excluded: chain AQ residue 3 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 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 Chi-restraints excluded: chain A7 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: 0.9990 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: 0.8944 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.118 0.617 5124 Z= 6.609 Angle : 4.531 38.741 7126 Z= 1.860 Chirality : 0.232 0.516 420 Planarity : 0.025 0.089 532 Dihedral : 37.463 89.685 658 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 56.82 Ramachandran Plot: Outliers : 2.98 % Allowed : 66.67 % Favored : 30.36 % Rotamer: Outliers : 21.98 % Allowed : 10.71 % Favored : 67.31 % Cbeta Deviations : 3.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.61 % 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: -10.87 (0.37), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.28 (0.28), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.074 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 86 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 6 time to evaluate : 0.444 Fit side-chains outliers start: 80 outliers final: 68 residues processed: 86 average time/residue: 0.0667 time to fit residues: 9.7666 Evaluate side-chains 73 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 5 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 3 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 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 3 residue 6 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain 6 residue 3 SER Chi-restraints excluded: chain 9 residue 3 SER Chi-restraints excluded: chain a residue 3 SER Chi-restraints excluded: chain b residue 3 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain g residue 3 SER Chi-restraints excluded: chain i residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain k residue 3 SER 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 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 y residue 3 SER Chi-restraints excluded: chain AB residue 3 SER Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AC residue 3 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AF residue 3 SER Chi-restraints excluded: chain AI residue 3 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 AM residue 3 SER Chi-restraints excluded: chain AQ residue 3 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 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 Chi-restraints excluded: chain A7 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: 0.9980 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: 0.8944 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.118 0.616 5124 Z= 6.608 Angle : 4.535 38.836 7126 Z= 1.861 Chirality : 0.233 0.522 420 Planarity : 0.025 0.089 532 Dihedral : 37.507 89.501 658 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 56.28 Ramachandran Plot: Outliers : 2.98 % Allowed : 66.07 % Favored : 30.95 % Rotamer: Outliers : 21.43 % Allowed : 10.99 % Favored : 67.58 % Cbeta Deviations : 3.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.61 % 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: -10.83 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.26 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.074 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 84 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 6 time to evaluate : 0.574 Fit side-chains outliers start: 78 outliers final: 68 residues processed: 84 average time/residue: 0.0796 time to fit residues: 11.2620 Evaluate side-chains 74 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 6 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 3 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 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 3 residue 6 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain 6 residue 3 SER Chi-restraints excluded: chain 9 residue 3 SER Chi-restraints excluded: chain a residue 3 SER Chi-restraints excluded: chain b residue 3 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain g residue 3 SER Chi-restraints excluded: chain i residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain k residue 3 SER 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 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 y residue 3 SER Chi-restraints excluded: chain AB residue 3 SER Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AC residue 3 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AF residue 3 SER Chi-restraints excluded: chain AI residue 3 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 AM residue 3 SER Chi-restraints excluded: chain AQ residue 3 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 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 Chi-restraints excluded: chain A7 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: 0.8944 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.118 0.617 5124 Z= 6.604 Angle : 4.533 38.802 7126 Z= 1.859 Chirality : 0.233 0.520 420 Planarity : 0.025 0.089 532 Dihedral : 37.534 89.476 658 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 56.00 Ramachandran Plot: Outliers : 2.98 % Allowed : 66.67 % Favored : 30.36 % Rotamer: Outliers : 20.33 % Allowed : 10.99 % Favored : 68.68 % Cbeta Deviations : 3.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.61 % 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: -10.84 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.26 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.074 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 79 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 5 time to evaluate : 0.460 Fit side-chains outliers start: 74 outliers final: 69 residues processed: 79 average time/residue: 0.0691 time to fit residues: 9.3913 Evaluate side-chains 74 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 5 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 3 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 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 3 residue 6 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain 6 residue 3 SER Chi-restraints excluded: chain 9 residue 3 SER Chi-restraints excluded: chain a residue 3 SER Chi-restraints excluded: chain b residue 3 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain g residue 3 SER Chi-restraints excluded: chain i residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain k residue 3 SER 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 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 y residue 3 SER Chi-restraints excluded: chain AB residue 3 SER Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AC residue 3 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AF residue 3 SER Chi-restraints excluded: chain AI residue 3 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 AM residue 3 SER Chi-restraints excluded: chain AQ residue 3 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 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 Chi-restraints excluded: chain A7 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: 0.8944 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.118 0.617 5124 Z= 6.612 Angle : 4.536 38.858 7126 Z= 1.860 Chirality : 0.233 0.520 420 Planarity : 0.025 0.089 532 Dihedral : 37.539 89.455 658 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 57.26 Ramachandran Plot: Outliers : 2.98 % Allowed : 66.67 % Favored : 30.36 % Rotamer: Outliers : 20.05 % Allowed : 11.81 % Favored : 68.13 % Cbeta Deviations : 3.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.61 % 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: -10.83 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.25 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.074 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 78 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 5 time to evaluate : 0.454 Fit side-chains outliers start: 73 outliers final: 68 residues processed: 78 average time/residue: 0.0658 time to fit residues: 8.7657 Evaluate side-chains 73 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 5 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 3 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 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 3 residue 6 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain 6 residue 3 SER Chi-restraints excluded: chain 9 residue 3 SER Chi-restraints excluded: chain a residue 3 SER Chi-restraints excluded: chain b residue 3 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain g residue 3 SER Chi-restraints excluded: chain i residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain k residue 3 SER 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 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 y residue 3 SER Chi-restraints excluded: chain AB residue 3 SER Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AC residue 3 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AF residue 3 SER Chi-restraints excluded: chain AI residue 3 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 AM residue 3 SER Chi-restraints excluded: chain AQ residue 3 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 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 Chi-restraints excluded: chain A7 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: 0.9980 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: 0.8944 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.118 0.617 5124 Z= 6.607 Angle : 4.533 38.736 7126 Z= 1.858 Chirality : 0.233 0.521 420 Planarity : 0.025 0.089 532 Dihedral : 37.549 89.445 658 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 56.69 Ramachandran Plot: Outliers : 2.98 % Allowed : 66.67 % Favored : 30.36 % Rotamer: Outliers : 18.68 % Allowed : 13.19 % Favored : 68.13 % Cbeta Deviations : 3.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.61 % 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: -10.84 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.26 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.074 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 73 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 5 time to evaluate : 0.416 Fit side-chains outliers start: 68 outliers final: 68 residues processed: 73 average time/residue: 0.0666 time to fit residues: 8.4284 Evaluate side-chains 73 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 5 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain C residue 3 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 3 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain 3 residue 3 SER Chi-restraints excluded: chain 3 residue 6 SER Chi-restraints excluded: chain 5 residue 3 SER Chi-restraints excluded: chain 5 residue 5 THR Chi-restraints excluded: chain 6 residue 3 SER Chi-restraints excluded: chain 9 residue 3 SER Chi-restraints excluded: chain a residue 3 SER Chi-restraints excluded: chain b residue 3 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain d residue 3 SER Chi-restraints excluded: chain g residue 3 SER Chi-restraints excluded: chain i residue 3 SER Chi-restraints excluded: chain j residue 3 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain k residue 3 SER 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 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 y residue 3 SER Chi-restraints excluded: chain AB residue 3 SER Chi-restraints excluded: chain AB residue 6 SER Chi-restraints excluded: chain AC residue 3 SER Chi-restraints excluded: chain AE residue 5 THR Chi-restraints excluded: chain AF residue 3 SER Chi-restraints excluded: chain AI residue 3 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 AM residue 3 SER Chi-restraints excluded: chain AQ residue 3 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 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 Chi-restraints excluded: chain A7 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 = 0.3206 r_free = 0.3206 target = 0.072021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.053206 restraints weight = 14265.445| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.58 r_work: 0.2602 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.118 0.617 5124 Z= 6.608 Angle : 4.533 38.778 7126 Z= 1.858 Chirality : 0.233 0.521 420 Planarity : 0.025 0.089 532 Dihedral : 37.552 89.442 658 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 57.12 Ramachandran Plot: Outliers : 2.98 % Allowed : 66.67 % Favored : 30.36 % Rotamer: Outliers : 19.78 % Allowed : 12.09 % Favored : 68.13 % Cbeta Deviations : 3.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.61 % 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: -10.84 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.26 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.074 0.015 TYR S 2 =============================================================================== Job complete usr+sys time: 613.05 seconds wall clock time: 12 minutes 22.12 seconds (742.12 seconds total)