Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 17:26:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/08_2023/7uuq_26800_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/08_2023/7uuq_26800.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/08_2023/7uuq_26800_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/08_2023/7uuq_26800_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/08_2023/7uuq_26800_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/08_2023/7uuq_26800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/08_2023/7uuq_26800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/08_2023/7uuq_26800_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuq_26800/08_2023/7uuq_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-1.21rc1-5044/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Planarities with less than four sites: {'OG9:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.31, per 1000 atoms: 0.49 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: 2.50 Conformation dependent library (CDL) restraints added in 243.2 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: 0.52 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: 2.62 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=" C SERA4 3 " pdb=" O SERA4 3 " ideal model delta sigma weight residual 1.238 1.200 0.038 1.28e-02 6.10e+03 8.65e+00 bond pdb=" C SER a 3 " pdb=" O SER a 3 " ideal model delta sigma weight residual 1.238 1.200 0.038 1.28e-02 6.10e+03 8.61e+00 bond pdb=" C SER 3 3 " pdb=" O SER 3 3 " ideal model delta sigma weight residual 1.238 1.200 0.037 1.28e-02 6.10e+03 8.58e+00 bond pdb=" C SER v 3 " pdb=" O SER v 3 " ideal model delta sigma weight residual 1.238 1.200 0.037 1.28e-02 6.10e+03 8.56e+00 bond pdb=" C SER h 3 " pdb=" O SER h 3 " ideal model delta sigma weight residual 1.238 1.200 0.037 1.28e-02 6.10e+03 8.56e+00 ... (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=" CA OG9AA 1 " pdb=" C05 OG9AA 1 " pdb=" C06 OG9AA 1 " ideal model delta sigma weight residual 104.18 120.63 -16.45 3.00e+00 1.11e-01 3.01e+01 angle pdb=" CA OG9 N 1 " pdb=" C05 OG9 N 1 " pdb=" C06 OG9 N 1 " ideal model delta sigma weight residual 104.18 120.59 -16.41 3.00e+00 1.11e-01 2.99e+01 angle pdb=" CA OG9AO 1 " pdb=" C05 OG9AO 1 " pdb=" C06 OG9AO 1 " ideal model delta sigma weight residual 104.18 120.59 -16.41 3.00e+00 1.11e-01 2.99e+01 angle pdb=" CA OG9 1 1 " pdb=" C05 OG9 1 1 " pdb=" C06 OG9 1 1 " ideal model delta sigma weight residual 104.18 120.58 -16.40 3.00e+00 1.11e-01 2.99e+01 angle pdb=" CA OG9A2 1 " pdb=" C05 OG9A2 1 " pdb=" C06 OG9A2 1 " ideal model delta sigma weight residual 104.18 120.58 -16.40 3.00e+00 1.11e-01 2.99e+01 ... (remaining 7121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 1554 15.90 - 31.79: 238 31.79 - 47.68: 42 47.68 - 63.58: 20 63.58 - 79.47: 36 Dihedral angle restraints: 1890 sinusoidal: 798 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 1887 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.750 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 15.170 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.120 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.070 ------------------------------------------------------------------------------- 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 : 0.014 0.051 5124 Z= 0.761 Angle : 2.950 16.446 7126 Z= 1.107 Chirality : 0.058 0.192 420 Planarity : 0.012 0.048 532 Dihedral : 20.394 79.473 1162 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 % 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 *********************** 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 : 0.470 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0895 time to fit residues: 12.1145 Evaluate side-chains 55 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4709 ------------------------------------------------------------------------------- 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: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.118 0.609 5124 Z= 6.624 Angle : 4.538 34.039 7126 Z= 1.863 Chirality : 0.232 0.475 420 Planarity : 0.022 0.078 532 Dihedral : 29.770 88.429 560 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 56.20 Ramachandran Plot: Outliers : 29.17 % Allowed : 39.29 % Favored : 31.55 % Rotamer Outliers : 11.26 % Cbeta Deviations : 1.92 % 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: -10.47 (0.46), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.98 (0.35), residues: 168 *********************** 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 50 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 9 time to evaluate : 0.427 Fit side-chains outliers start: 41 outliers final: 35 residues processed: 50 average time/residue: 0.0631 time to fit residues: 5.6290 Evaluate side-chains 43 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 8 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.0455 time to fit residues: 3.3439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8942 moved from start: 0.5330 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= 6.636 Angle : 4.678 34.621 7126 Z= 1.905 Chirality : 0.231 0.514 420 Planarity : 0.025 0.088 532 Dihedral : 29.077 88.714 560 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 53.31 Ramachandran Plot: Outliers : 2.98 % Allowed : 67.26 % Favored : 29.76 % Rotamer Outliers : 17.03 % Cbeta Deviations : 2.75 % 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: -10.82 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.24 (0.29), residues: 168 *********************** 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 67 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 5 time to evaluate : 0.486 Fit side-chains outliers start: 62 outliers final: 44 residues processed: 67 average time/residue: 0.0648 time to fit residues: 7.7001 Evaluate side-chains 49 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 5 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.0508 time to fit residues: 4.4721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8942 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.118 0.611 5124 Z= 6.635 Angle : 4.685 34.557 7126 Z= 1.901 Chirality : 0.230 0.520 420 Planarity : 0.024 0.082 532 Dihedral : 28.796 89.732 560 Min Nonbonded Distance : 1.579 Molprobity Statistics. All-atom Clashscore : 52.74 Ramachandran Plot: Outliers : 2.98 % Allowed : 66.67 % Favored : 30.36 % Rotamer Outliers : 16.76 % 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: -10.64 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.10 (0.31), residues: 168 *********************** 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 70 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 9 time to evaluate : 0.432 Fit side-chains outliers start: 61 outliers final: 51 residues processed: 66 average time/residue: 0.0659 time to fit residues: 7.5049 Evaluate side-chains 59 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 8 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.0452 time to fit residues: 4.7146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8943 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.118 0.614 5124 Z= 6.643 Angle : 4.683 34.579 7126 Z= 1.903 Chirality : 0.231 0.524 420 Planarity : 0.025 0.083 532 Dihedral : 28.816 89.655 560 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 53.03 Ramachandran Plot: Outliers : 3.57 % Allowed : 64.88 % Favored : 31.55 % Rotamer Outliers : 15.38 % 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: -10.58 (0.42), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.06 (0.32), residues: 168 *********************** 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 66 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 10 time to evaluate : 0.469 Fit side-chains outliers start: 56 outliers final: 40 residues processed: 63 average time/residue: 0.0654 time to fit residues: 7.2253 Evaluate side-chains 51 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 11 time to evaluate : 0.456 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.0467 time to fit residues: 3.8968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.5438 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= 6.649 Angle : 4.697 34.875 7126 Z= 1.908 Chirality : 0.231 0.520 420 Planarity : 0.025 0.084 532 Dihedral : 28.816 89.679 560 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 56.37 Ramachandran Plot: Outliers : 3.57 % Allowed : 65.48 % Favored : 30.95 % Rotamer Outliers : 11.26 % 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: -10.65 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.11 (0.31), residues: 168 *********************** 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 51 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 10 time to evaluate : 0.443 Fit side-chains outliers start: 41 outliers final: 29 residues processed: 46 average time/residue: 0.0671 time to fit residues: 5.5678 Evaluate side-chains 38 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 9 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.0495 time to fit residues: 3.0802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8941 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.118 0.618 5124 Z= 6.643 Angle : 4.700 34.528 7126 Z= 1.910 Chirality : 0.232 0.520 420 Planarity : 0.025 0.085 532 Dihedral : 28.844 89.595 560 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 54.83 Ramachandran Plot: Outliers : 2.38 % Allowed : 66.67 % Favored : 30.95 % Rotamer Outliers : 8.79 % Cbeta Deviations : 2.75 % 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: -10.63 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.10 (0.32), residues: 168 *********************** 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 44 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 12 time to evaluate : 0.421 Fit side-chains outliers start: 32 outliers final: 21 residues processed: 43 average time/residue: 0.0643 time to fit residues: 5.0237 Evaluate side-chains 33 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 12 time to evaluate : 0.461 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0453 time to fit residues: 2.1919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8941 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.118 0.621 5124 Z= 6.644 Angle : 4.703 34.513 7126 Z= 1.913 Chirality : 0.232 0.519 420 Planarity : 0.025 0.085 532 Dihedral : 28.814 89.653 560 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 53.99 Ramachandran Plot: Outliers : 3.57 % Allowed : 64.88 % Favored : 31.55 % Rotamer Outliers : 6.04 % 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: -10.63 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.10 (0.31), residues: 168 *********************** 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 35 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 13 time to evaluate : 0.431 Fit side-chains outliers start: 22 outliers final: 18 residues processed: 30 average time/residue: 0.0668 time to fit residues: 3.7727 Evaluate side-chains 28 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 10 time to evaluate : 0.480 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0471 time to fit residues: 2.0245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8941 moved from start: 0.5479 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= 6.636 Angle : 4.705 34.868 7126 Z= 1.917 Chirality : 0.231 0.518 420 Planarity : 0.025 0.085 532 Dihedral : 28.826 89.624 560 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 54.42 Ramachandran Plot: Outliers : 2.98 % Allowed : 65.48 % Favored : 31.55 % Rotamer Outliers : 2.20 % 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: -10.63 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.10 (0.31), residues: 168 *********************** 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 20 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 12 time to evaluate : 0.445 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 19 average time/residue: 0.0688 time to fit residues: 2.7519 Evaluate side-chains 19 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 12 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0462 time to fit residues: 1.0552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8941 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.118 0.620 5124 Z= 6.639 Angle : 4.703 35.017 7126 Z= 1.912 Chirality : 0.231 0.518 420 Planarity : 0.025 0.083 532 Dihedral : 28.807 89.623 560 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 53.03 Ramachandran Plot: Outliers : 2.98 % Allowed : 65.48 % Favored : 31.55 % Rotamer Outliers : 3.02 % 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: -10.61 (0.42), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.08 (0.32), residues: 168 ********************** 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 26 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 15 time to evaluate : 0.481 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 22 average time/residue: 0.0694 time to fit residues: 3.0895 Evaluate side-chains 20 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 12 time to evaluate : 0.482 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0479 time to fit residues: 1.1709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.074692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.055489 restraints weight = 14734.676| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.56 r_work: 0.2614 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.118 0.620 5124 Z= 6.638 Angle : 4.703 35.165 7126 Z= 1.915 Chirality : 0.231 0.518 420 Planarity : 0.025 0.084 532 Dihedral : 28.812 89.607 560 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 53.03 Ramachandran Plot: Outliers : 2.98 % Allowed : 65.48 % Favored : 31.55 % Rotamer Outliers : 1.10 % 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: -10.62 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.09 (0.32), residues: 168 =============================================================================== Job complete usr+sys time: 558.73 seconds wall clock time: 11 minutes 23.98 seconds (683.98 seconds total)