Starting phenix.real_space_refine on Sat Dec 16 00:46:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m54_30084/12_2023/6m54_30084_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m54_30084/12_2023/6m54_30084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m54_30084/12_2023/6m54_30084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m54_30084/12_2023/6m54_30084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m54_30084/12_2023/6m54_30084_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m54_30084/12_2023/6m54_30084_updated.pdb" } resolution = 2.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 168 5.16 5 C 20978 2.51 5 N 5886 2.21 5 O 6344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "J GLU 68": "OE1" <-> "OE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "L GLU 68": "OE1" <-> "OE2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "P ARG 64": "NH1" <-> "NH2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "Q GLU 68": "OE1" <-> "OE2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "W GLU 95": "OE1" <-> "OE2" Residue "X GLU 68": "OE1" <-> "OE2" Residue "X GLU 95": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 33382 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "B" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "D" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "E" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "G" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "H" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "J" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "M" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "N" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "O" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "Q" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "R" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "S" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "T" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 22.44, per 1000 atoms: 0.67 Number of scatterers: 33382 At special positions: 0 Unit cell: (136.59, 136.59, 136.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 6 26.01 S 168 16.00 O 6344 8.00 N 5886 7.00 C 20978 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=0, symmetry=0 Time building additional restraints: 10.92 Conformation dependent library (CDL) restraints added in 8.1 seconds 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7892 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 0 sheets defined 73.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 removed outlier: 3.765A pdb=" N ASN A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 77 removed outlier: 3.571A pdb=" N ARG A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 124 removed outlier: 3.640A pdb=" N ASN A 110 " --> pdb=" O HIS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 Processing helix chain 'A' and resid 139 through 159 removed outlier: 3.729A pdb=" N VAL A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'B' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.723A pdb=" N ARG B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 124 removed outlier: 3.570A pdb=" N MET B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B 110 " --> pdb=" O HIS B 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 159 removed outlier: 4.058A pdb=" N LEU B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASN B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'C' and resid 15 through 41 removed outlier: 3.689A pdb=" N ASN C 26 " --> pdb=" O ASN C 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 77 removed outlier: 3.684A pdb=" N ARG C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 65 " --> pdb=" O HIS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 124 removed outlier: 3.617A pdb=" N ASN C 110 " --> pdb=" O HIS C 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 159 removed outlier: 4.081A pdb=" N LEU C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN C 140 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 142 " --> pdb=" O TYR C 138 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'D' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 77 removed outlier: 3.685A pdb=" N ARG D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 65 " --> pdb=" O HIS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 124 removed outlier: 3.571A pdb=" N MET D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 159 removed outlier: 4.083A pdb=" N LEU D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN D 140 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU D 141 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN D 142 " --> pdb=" O TYR D 138 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'E' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 77 removed outlier: 3.720A pdb=" N ARG E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU E 65 " --> pdb=" O HIS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 124 removed outlier: 3.570A pdb=" N MET E 101 " --> pdb=" O GLY E 97 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN E 110 " --> pdb=" O HIS E 106 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 159 removed outlier: 4.059A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN E 140 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU E 141 " --> pdb=" O HIS E 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN E 142 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 174 Processing helix chain 'F' and resid 15 through 41 removed outlier: 3.689A pdb=" N ASN F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.683A pdb=" N ARG F 64 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 124 removed outlier: 3.618A pdb=" N ASN F 110 " --> pdb=" O HIS F 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 159 removed outlier: 4.082A pdb=" N LEU F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN F 140 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN F 142 " --> pdb=" O TYR F 138 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 Processing helix chain 'G' and resid 15 through 41 removed outlier: 3.689A pdb=" N ASN G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 77 removed outlier: 3.684A pdb=" N ARG G 64 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU G 65 " --> pdb=" O HIS G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 124 removed outlier: 3.570A pdb=" N MET G 101 " --> pdb=" O GLY G 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN G 110 " --> pdb=" O HIS G 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 159 removed outlier: 4.084A pdb=" N LEU G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN G 140 " --> pdb=" O THR G 136 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU G 141 " --> pdb=" O HIS G 137 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN G 142 " --> pdb=" O TYR G 138 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'H' and resid 15 through 41 removed outlier: 3.689A pdb=" N ASN H 26 " --> pdb=" O ASN H 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 77 removed outlier: 3.704A pdb=" N ARG H 64 " --> pdb=" O SER H 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU H 65 " --> pdb=" O HIS H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 124 removed outlier: 3.569A pdb=" N MET H 101 " --> pdb=" O GLY H 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN H 110 " --> pdb=" O HIS H 106 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU H 117 " --> pdb=" O GLN H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 159 removed outlier: 4.060A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN H 140 " --> pdb=" O THR H 136 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU H 141 " --> pdb=" O HIS H 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN H 142 " --> pdb=" O TYR H 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 174 Processing helix chain 'I' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN I 26 " --> pdb=" O ASN I 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 77 removed outlier: 3.683A pdb=" N ARG I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU I 65 " --> pdb=" O HIS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 124 removed outlier: 3.563A pdb=" N MET I 101 " --> pdb=" O GLY I 97 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN I 110 " --> pdb=" O HIS I 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU I 117 " --> pdb=" O GLN I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 159 removed outlier: 4.084A pdb=" N LEU I 139 " --> pdb=" O GLU I 135 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN I 140 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU I 141 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN I 142 " --> pdb=" O TYR I 138 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL I 143 " --> pdb=" O LEU I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 174 Processing helix chain 'J' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN J 26 " --> pdb=" O ASN J 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 77 removed outlier: 3.720A pdb=" N ARG J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU J 65 " --> pdb=" O HIS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 124 removed outlier: 3.569A pdb=" N MET J 101 " --> pdb=" O GLY J 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN J 110 " --> pdb=" O HIS J 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 159 removed outlier: 4.059A pdb=" N LEU J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN J 140 " --> pdb=" O THR J 136 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU J 141 " --> pdb=" O HIS J 137 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN J 142 " --> pdb=" O TYR J 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 174 Processing helix chain 'K' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN K 26 " --> pdb=" O ASN K 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 77 removed outlier: 3.704A pdb=" N ARG K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU K 65 " --> pdb=" O HIS K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 124 removed outlier: 3.567A pdb=" N MET K 101 " --> pdb=" O GLY K 97 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN K 110 " --> pdb=" O HIS K 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU K 117 " --> pdb=" O GLN K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 159 removed outlier: 4.059A pdb=" N LEU K 139 " --> pdb=" O GLU K 135 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU K 141 " --> pdb=" O HIS K 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN K 142 " --> pdb=" O TYR K 138 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL K 143 " --> pdb=" O LEU K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 174 Processing helix chain 'L' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN L 26 " --> pdb=" O ASN L 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 77 removed outlier: 3.683A pdb=" N ARG L 64 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU L 65 " --> pdb=" O HIS L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 124 removed outlier: 3.570A pdb=" N MET L 101 " --> pdb=" O GLY L 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN L 110 " --> pdb=" O HIS L 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU L 117 " --> pdb=" O GLN L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 159 removed outlier: 4.081A pdb=" N LEU L 139 " --> pdb=" O GLU L 135 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN L 140 " --> pdb=" O THR L 136 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU L 141 " --> pdb=" O HIS L 137 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN L 142 " --> pdb=" O TYR L 138 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 174 Processing helix chain 'M' and resid 15 through 41 removed outlier: 3.689A pdb=" N ASN M 26 " --> pdb=" O ASN M 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 77 removed outlier: 3.683A pdb=" N ARG M 64 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU M 65 " --> pdb=" O HIS M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 124 removed outlier: 3.563A pdb=" N MET M 101 " --> pdb=" O GLY M 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN M 110 " --> pdb=" O HIS M 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU M 117 " --> pdb=" O GLN M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 159 removed outlier: 4.083A pdb=" N LEU M 139 " --> pdb=" O GLU M 135 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN M 140 " --> pdb=" O THR M 136 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU M 141 " --> pdb=" O HIS M 137 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN M 142 " --> pdb=" O TYR M 138 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL M 143 " --> pdb=" O LEU M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 174 Processing helix chain 'N' and resid 15 through 41 removed outlier: 3.689A pdb=" N ASN N 26 " --> pdb=" O ASN N 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 77 removed outlier: 3.683A pdb=" N ARG N 64 " --> pdb=" O SER N 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU N 65 " --> pdb=" O HIS N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 124 removed outlier: 3.570A pdb=" N MET N 101 " --> pdb=" O GLY N 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN N 110 " --> pdb=" O HIS N 106 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU N 117 " --> pdb=" O GLN N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 159 removed outlier: 4.081A pdb=" N LEU N 139 " --> pdb=" O GLU N 135 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN N 140 " --> pdb=" O THR N 136 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU N 141 " --> pdb=" O HIS N 137 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN N 142 " --> pdb=" O TYR N 138 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL N 143 " --> pdb=" O LEU N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 174 Processing helix chain 'O' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN O 26 " --> pdb=" O ASN O 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 77 removed outlier: 3.721A pdb=" N ARG O 64 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU O 65 " --> pdb=" O HIS O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 124 removed outlier: 3.569A pdb=" N MET O 101 " --> pdb=" O GLY O 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN O 110 " --> pdb=" O HIS O 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 159 removed outlier: 4.052A pdb=" N LEU O 139 " --> pdb=" O GLU O 135 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN O 140 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU O 141 " --> pdb=" O HIS O 137 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN O 142 " --> pdb=" O TYR O 138 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL O 143 " --> pdb=" O LEU O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 174 Processing helix chain 'P' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN P 26 " --> pdb=" O ASN P 22 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 77 removed outlier: 3.721A pdb=" N ARG P 64 " --> pdb=" O SER P 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU P 65 " --> pdb=" O HIS P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 124 removed outlier: 3.556A pdb=" N MET P 101 " --> pdb=" O GLY P 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN P 110 " --> pdb=" O HIS P 106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 159 removed outlier: 4.059A pdb=" N LEU P 139 " --> pdb=" O GLU P 135 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN P 140 " --> pdb=" O THR P 136 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU P 141 " --> pdb=" O HIS P 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN P 142 " --> pdb=" O TYR P 138 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL P 143 " --> pdb=" O LEU P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 174 Processing helix chain 'Q' and resid 15 through 41 removed outlier: 3.689A pdb=" N ASN Q 26 " --> pdb=" O ASN Q 22 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 77 removed outlier: 3.683A pdb=" N ARG Q 64 " --> pdb=" O SER Q 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU Q 65 " --> pdb=" O HIS Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 124 removed outlier: 3.572A pdb=" N MET Q 101 " --> pdb=" O GLY Q 97 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN Q 110 " --> pdb=" O HIS Q 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 159 removed outlier: 4.083A pdb=" N LEU Q 139 " --> pdb=" O GLU Q 135 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN Q 140 " --> pdb=" O THR Q 136 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU Q 141 " --> pdb=" O HIS Q 137 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN Q 142 " --> pdb=" O TYR Q 138 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 174 Processing helix chain 'R' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN R 26 " --> pdb=" O ASN R 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 77 removed outlier: 3.704A pdb=" N ARG R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU R 65 " --> pdb=" O HIS R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 124 removed outlier: 3.569A pdb=" N MET R 101 " --> pdb=" O GLY R 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN R 110 " --> pdb=" O HIS R 106 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU R 117 " --> pdb=" O GLN R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 159 removed outlier: 4.059A pdb=" N LEU R 139 " --> pdb=" O GLU R 135 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN R 140 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU R 141 " --> pdb=" O HIS R 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN R 142 " --> pdb=" O TYR R 138 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL R 143 " --> pdb=" O LEU R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 174 Processing helix chain 'S' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN S 26 " --> pdb=" O ASN S 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 50 through 77 removed outlier: 3.722A pdb=" N ARG S 64 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU S 65 " --> pdb=" O HIS S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 124 removed outlier: 3.619A pdb=" N ASN S 110 " --> pdb=" O HIS S 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU S 117 " --> pdb=" O GLN S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 159 removed outlier: 4.058A pdb=" N LEU S 139 " --> pdb=" O GLU S 135 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASN S 140 " --> pdb=" O THR S 136 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU S 141 " --> pdb=" O HIS S 137 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN S 142 " --> pdb=" O TYR S 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL S 143 " --> pdb=" O LEU S 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 174 Processing helix chain 'T' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN T 26 " --> pdb=" O ASN T 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR T 40 " --> pdb=" O LEU T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 77 removed outlier: 3.704A pdb=" N ARG T 64 " --> pdb=" O SER T 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU T 65 " --> pdb=" O HIS T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 124 removed outlier: 3.569A pdb=" N MET T 101 " --> pdb=" O GLY T 97 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN T 110 " --> pdb=" O HIS T 106 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU T 117 " --> pdb=" O GLN T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 128 through 159 removed outlier: 4.058A pdb=" N LEU T 139 " --> pdb=" O GLU T 135 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASN T 140 " --> pdb=" O THR T 136 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU T 141 " --> pdb=" O HIS T 137 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN T 142 " --> pdb=" O TYR T 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL T 143 " --> pdb=" O LEU T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 174 Processing helix chain 'U' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN U 26 " --> pdb=" O ASN U 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 50 through 77 removed outlier: 3.721A pdb=" N ARG U 64 " --> pdb=" O SER U 60 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 124 removed outlier: 3.618A pdb=" N ASN U 110 " --> pdb=" O HIS U 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU U 117 " --> pdb=" O GLN U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 159 removed outlier: 4.058A pdb=" N LEU U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASN U 140 " --> pdb=" O THR U 136 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU U 141 " --> pdb=" O HIS U 137 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN U 142 " --> pdb=" O TYR U 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL U 143 " --> pdb=" O LEU U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 165 through 174 Processing helix chain 'V' and resid 15 through 41 removed outlier: 3.689A pdb=" N ASN V 26 " --> pdb=" O ASN V 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR V 40 " --> pdb=" O LEU V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 77 removed outlier: 3.725A pdb=" N ARG V 64 " --> pdb=" O SER V 60 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 124 removed outlier: 3.617A pdb=" N ASN V 110 " --> pdb=" O HIS V 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU V 117 " --> pdb=" O GLN V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 128 through 159 removed outlier: 4.059A pdb=" N LEU V 139 " --> pdb=" O GLU V 135 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN V 140 " --> pdb=" O THR V 136 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU V 141 " --> pdb=" O HIS V 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN V 142 " --> pdb=" O TYR V 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL V 143 " --> pdb=" O LEU V 139 " (cutoff:3.500A) Processing helix chain 'V' and resid 165 through 174 Processing helix chain 'W' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN W 26 " --> pdb=" O ASN W 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR W 40 " --> pdb=" O LEU W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 77 removed outlier: 3.722A pdb=" N ARG W 64 " --> pdb=" O SER W 60 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU W 65 " --> pdb=" O HIS W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 124 removed outlier: 3.615A pdb=" N ASN W 110 " --> pdb=" O HIS W 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU W 117 " --> pdb=" O GLN W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 159 removed outlier: 4.058A pdb=" N LEU W 139 " --> pdb=" O GLU W 135 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASN W 140 " --> pdb=" O THR W 136 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU W 141 " --> pdb=" O HIS W 137 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN W 142 " --> pdb=" O TYR W 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 165 through 174 Processing helix chain 'X' and resid 15 through 41 removed outlier: 3.690A pdb=" N ASN X 26 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR X 40 " --> pdb=" O LEU X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 77 removed outlier: 3.704A pdb=" N ARG X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU X 65 " --> pdb=" O HIS X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 124 removed outlier: 3.615A pdb=" N ASN X 110 " --> pdb=" O HIS X 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU X 117 " --> pdb=" O GLN X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 159 removed outlier: 4.058A pdb=" N LEU X 139 " --> pdb=" O GLU X 135 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASN X 140 " --> pdb=" O THR X 136 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU X 141 " --> pdb=" O HIS X 137 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN X 142 " --> pdb=" O TYR X 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL X 143 " --> pdb=" O LEU X 139 " (cutoff:3.500A) Processing helix chain 'X' and resid 165 through 174 2241 hydrogen bonds defined for protein. 6723 hydrogen bond angles 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: 8.91 Time building geometry restraints manager: 12.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7349 1.33 - 1.44: 7729 1.44 - 1.56: 18732 1.56 - 1.68: 0 1.68 - 1.80: 264 Bond restraints: 34074 Sorted by residual: bond pdb=" CB LYS X 69 " pdb=" CG LYS X 69 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.97e+00 bond pdb=" CB LYS B 69 " pdb=" CG LYS B 69 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.90e+00 bond pdb=" CB LYS W 69 " pdb=" CG LYS W 69 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.88e+00 bond pdb=" CB LYS O 69 " pdb=" CG LYS O 69 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.88e+00 bond pdb=" CB LYS R 69 " pdb=" CG LYS R 69 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.86e+00 ... (remaining 34069 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.45: 558 106.45 - 113.32: 16914 113.32 - 120.19: 15148 120.19 - 127.06: 12997 127.06 - 133.93: 353 Bond angle restraints: 45970 Sorted by residual: angle pdb=" N GLU X 95 " pdb=" CA GLU X 95 " pdb=" C GLU X 95 " ideal model delta sigma weight residual 110.80 121.35 -10.55 2.13e+00 2.20e-01 2.45e+01 angle pdb=" N GLU W 95 " pdb=" CA GLU W 95 " pdb=" C GLU W 95 " ideal model delta sigma weight residual 110.80 121.33 -10.53 2.13e+00 2.20e-01 2.44e+01 angle pdb=" N GLU C 95 " pdb=" CA GLU C 95 " pdb=" C GLU C 95 " ideal model delta sigma weight residual 110.80 121.30 -10.50 2.13e+00 2.20e-01 2.43e+01 angle pdb=" N GLU F 95 " pdb=" CA GLU F 95 " pdb=" C GLU F 95 " ideal model delta sigma weight residual 110.80 121.09 -10.29 2.13e+00 2.20e-01 2.34e+01 angle pdb=" C HIS A 137 " pdb=" N TYR A 138 " pdb=" CA TYR A 138 " ideal model delta sigma weight residual 122.42 114.63 7.79 1.77e+00 3.19e-01 1.93e+01 ... (remaining 45965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 18144 16.46 - 32.92: 1794 32.92 - 49.38: 519 49.38 - 65.84: 57 65.84 - 82.30: 48 Dihedral angle restraints: 20562 sinusoidal: 8354 harmonic: 12208 Sorted by residual: dihedral pdb=" CA TYR G 138 " pdb=" C TYR G 138 " pdb=" N LEU G 139 " pdb=" CA LEU G 139 " ideal model delta harmonic sigma weight residual -180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA TYR I 138 " pdb=" C TYR I 138 " pdb=" N LEU I 139 " pdb=" CA LEU I 139 " ideal model delta harmonic sigma weight residual -180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA TYR M 138 " pdb=" C TYR M 138 " pdb=" N LEU M 139 " pdb=" CA LEU M 139 " ideal model delta harmonic sigma weight residual -180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 20559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2104 0.047 - 0.094: 1865 0.094 - 0.142: 654 0.142 - 0.189: 186 0.189 - 0.236: 49 Chirality restraints: 4858 Sorted by residual: chirality pdb=" CG LEU A 73 " pdb=" CB LEU A 73 " pdb=" CD1 LEU A 73 " pdb=" CD2 LEU A 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CG LEU L 73 " pdb=" CB LEU L 73 " pdb=" CD1 LEU L 73 " pdb=" CD2 LEU L 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU N 73 " pdb=" CB LEU N 73 " pdb=" CD1 LEU N 73 " pdb=" CD2 LEU N 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4855 not shown) Planarity restraints: 6068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 33 " 0.034 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR B 33 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR B 33 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 33 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 33 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 33 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 33 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 33 " 0.034 2.00e-02 2.50e+03 2.80e-02 1.57e+01 pdb=" CG TYR S 33 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR S 33 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR S 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR S 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR S 33 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR S 33 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR S 33 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 33 " -0.034 2.00e-02 2.50e+03 2.80e-02 1.57e+01 pdb=" CG TYR E 33 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR E 33 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR E 33 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR E 33 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 33 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 33 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR E 33 " -0.003 2.00e-02 2.50e+03 ... (remaining 6065 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 18513 3.05 - 3.51: 31254 3.51 - 3.98: 51684 3.98 - 4.44: 63531 4.44 - 4.90: 92886 Nonbonded interactions: 257868 Sorted by model distance: nonbonded pdb=" O HIS A 137 " pdb=" CA TYR A 138 " model vdw 2.591 2.776 nonbonded pdb=" N SER W 96 " pdb=" O SER W 96 " model vdw 2.611 2.496 nonbonded pdb=" N SER X 96 " pdb=" O SER X 96 " model vdw 2.612 2.496 nonbonded pdb=" N SER C 96 " pdb=" O SER C 96 " model vdw 2.613 2.496 nonbonded pdb=" N ASP U 46 " pdb=" OD1 ASP U 46 " model vdw 2.615 2.520 ... (remaining 257863 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 'A' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'B' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'C' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'D' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'E' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'F' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'G' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'H' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'I' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'J' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'K' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'L' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'M' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'N' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'O' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'P' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'Q' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'R' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'S' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'T' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'U' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'V' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'W' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'X' and (resid 6 through 63 or resid 65 through 176)) } 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=0.50 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 6.760 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 86.370 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.012 0.070 34074 Z= 0.768 Angle : 1.145 10.547 45970 Z= 0.685 Chirality : 0.071 0.236 4858 Planarity : 0.006 0.054 6068 Dihedral : 14.960 82.302 12670 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.37 (0.11), residues: 4066 helix: 0.43 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -2.30 (0.14), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 94 HIS 0.005 0.002 HIS R 66 PHE 0.018 0.006 PHE A 56 TYR 0.068 0.006 TYR B 33 ARG 0.002 0.000 ARG R 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 3.943 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 2.2832 time to fit residues: 1235.6189 Evaluate side-chains 397 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 3.971 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 5.9990 chunk 309 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 208 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 319 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 238 optimal weight: 0.9980 chunk 370 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 15 GLN A 51 ASN A 110 ASN A 113 GLN B 14 HIS B 15 GLN B 51 ASN B 110 ASN B 113 GLN C 14 HIS C 15 GLN C 51 ASN C 110 ASN C 113 GLN D 14 HIS D 15 GLN D 51 ASN D 110 ASN D 113 GLN E 14 HIS E 15 GLN E 51 ASN E 110 ASN E 113 GLN F 14 HIS F 15 GLN F 51 ASN F 110 ASN F 113 GLN G 14 HIS G 15 GLN G 51 ASN G 110 ASN G 113 GLN H 14 HIS H 15 GLN H 51 ASN H 110 ASN H 113 GLN I 14 HIS I 15 GLN I 51 ASN I 110 ASN I 113 GLN J 14 HIS J 15 GLN J 51 ASN J 110 ASN J 113 GLN K 14 HIS K 15 GLN K 51 ASN K 110 ASN K 113 GLN L 14 HIS L 15 GLN L 51 ASN L 110 ASN L 113 GLN M 14 HIS M 15 GLN M 51 ASN M 110 ASN M 113 GLN N 14 HIS N 15 GLN N 51 ASN N 110 ASN N 113 GLN O 14 HIS O 15 GLN O 51 ASN O 110 ASN O 113 GLN P 14 HIS P 15 GLN P 51 ASN P 110 ASN P 113 GLN Q 14 HIS Q 15 GLN Q 51 ASN Q 110 ASN Q 113 GLN R 14 HIS R 15 GLN R 51 ASN R 110 ASN R 113 GLN S 14 HIS S 15 GLN S 51 ASN S 110 ASN S 113 GLN T 14 HIS T 15 GLN T 51 ASN T 110 ASN T 113 GLN U 14 HIS U 15 GLN U 51 ASN U 110 ASN U 113 GLN V 14 HIS V 15 GLN V 51 ASN V 110 ASN V 113 GLN W 14 HIS W 15 GLN W 51 ASN W 110 ASN W 113 GLN X 14 HIS X 15 GLN X 51 ASN X 110 ASN X 113 GLN Total number of N/Q/H flips: 120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34074 Z= 0.167 Angle : 0.514 5.874 45970 Z= 0.298 Chirality : 0.037 0.131 4858 Planarity : 0.003 0.028 6068 Dihedral : 4.205 22.238 4494 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.06 % Allowed : 5.54 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.03 (0.12), residues: 4066 helix: 3.19 (0.08), residues: 3034 sheet: None (None), residues: 0 loop : -1.93 (0.14), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 94 HIS 0.002 0.001 HIS A 14 PHE 0.008 0.001 PHE A 133 TYR 0.015 0.002 TYR V 33 ARG 0.002 0.000 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 510 time to evaluate : 4.526 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 512 average time/residue: 2.0425 time to fit residues: 1200.2401 Evaluate side-chains 426 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 4.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 308 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 371 optimal weight: 0.9990 chunk 400 optimal weight: 9.9990 chunk 330 optimal weight: 1.9990 chunk 368 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 297 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN D 113 GLN E 113 GLN F 113 GLN G 113 GLN H 113 GLN I 113 GLN J 113 GLN K 113 GLN L 113 GLN M 113 GLN N 113 GLN O 113 GLN P 113 GLN Q 113 GLN R 113 GLN S 113 GLN T 113 GLN U 113 GLN V 113 GLN W 113 GLN X 113 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34074 Z= 0.193 Angle : 0.529 6.160 45970 Z= 0.305 Chirality : 0.039 0.136 4858 Planarity : 0.003 0.022 6068 Dihedral : 4.201 22.586 4494 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.99 % Allowed : 8.65 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.65 (0.12), residues: 4066 helix: 3.64 (0.08), residues: 3034 sheet: None (None), residues: 0 loop : -1.74 (0.15), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 94 HIS 0.002 0.000 HIS A 14 PHE 0.009 0.002 PHE A 133 TYR 0.016 0.002 TYR H 33 ARG 0.001 0.000 ARG S 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 452 time to evaluate : 4.159 Fit side-chains outliers start: 35 outliers final: 34 residues processed: 452 average time/residue: 2.0700 time to fit residues: 1067.9057 Evaluate side-chains 466 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 432 time to evaluate : 3.939 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 1.6391 time to fit residues: 70.3730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 249 optimal weight: 0.6980 chunk 372 optimal weight: 6.9990 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 353 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 113 GLN E 113 GLN H 113 GLN J 113 GLN K 113 GLN O 113 GLN P 113 GLN R 113 GLN S 113 GLN T 113 GLN U 113 GLN V 113 GLN W 113 GLN X 113 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34074 Z= 0.185 Angle : 0.514 6.426 45970 Z= 0.297 Chirality : 0.038 0.139 4858 Planarity : 0.003 0.021 6068 Dihedral : 4.121 22.650 4494 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.99 % Allowed : 9.19 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.97 (0.12), residues: 4066 helix: 3.88 (0.08), residues: 3034 sheet: None (None), residues: 0 loop : -1.62 (0.15), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 94 HIS 0.001 0.000 HIS A 14 PHE 0.009 0.002 PHE A 133 TYR 0.014 0.002 TYR A 40 ARG 0.001 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 452 time to evaluate : 4.123 Fit side-chains outliers start: 35 outliers final: 19 residues processed: 467 average time/residue: 2.0044 time to fit residues: 1071.6344 Evaluate side-chains 439 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 420 time to evaluate : 3.861 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 1.9776 time to fit residues: 47.9755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 293 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 336 optimal weight: 2.9990 chunk 272 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 4.9990 chunk 353 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 113 GLN C 113 GLN E 113 GLN H 113 GLN H 140 ASN J 113 GLN J 140 ASN K 113 GLN K 140 ASN O 113 GLN P 113 GLN P 140 ASN R 113 GLN S 113 GLN T 113 GLN U 113 GLN V 113 GLN W 113 GLN X 113 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34074 Z= 0.185 Angle : 0.511 6.702 45970 Z= 0.295 Chirality : 0.038 0.143 4858 Planarity : 0.003 0.020 6068 Dihedral : 4.105 22.710 4494 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.41 % Allowed : 9.84 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.09 (0.12), residues: 4066 helix: 3.96 (0.08), residues: 3034 sheet: None (None), residues: 0 loop : -1.56 (0.15), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 94 HIS 0.001 0.000 HIS G 58 PHE 0.009 0.002 PHE A 133 TYR 0.014 0.002 TYR A 40 ARG 0.001 0.000 ARG V 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 434 time to evaluate : 4.433 Fit side-chains outliers start: 50 outliers final: 45 residues processed: 441 average time/residue: 2.1155 time to fit residues: 1063.6205 Evaluate side-chains 466 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 421 time to evaluate : 3.859 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 4 residues processed: 41 average time/residue: 1.6235 time to fit residues: 83.6198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 3.9990 chunk 355 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 394 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 113 GLN E 113 GLN E 140 ASN H 113 GLN J 113 GLN K 113 GLN O 113 GLN P 113 GLN R 113 GLN R 140 ASN S 113 GLN T 113 GLN U 113 GLN V 113 GLN V 140 ASN W 113 GLN X 113 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 34074 Z= 0.313 Angle : 0.653 6.636 45970 Z= 0.375 Chirality : 0.045 0.148 4858 Planarity : 0.004 0.027 6068 Dihedral : 4.388 23.397 4494 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.24 % Allowed : 11.31 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.40 (0.12), residues: 4066 helix: 3.40 (0.08), residues: 3058 sheet: None (None), residues: 0 loop : -1.73 (0.15), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 94 HIS 0.002 0.001 HIS M 106 PHE 0.011 0.003 PHE A 133 TYR 0.019 0.003 TYR U 40 ARG 0.003 0.001 ARG W 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 443 time to evaluate : 3.931 Fit side-chains outliers start: 44 outliers final: 25 residues processed: 451 average time/residue: 2.1438 time to fit residues: 1098.9408 Evaluate side-chains 448 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 423 time to evaluate : 3.985 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 1.9898 time to fit residues: 62.4467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 288 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 0.5980 chunk 239 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 113 GLN D 113 GLN E 113 GLN F 113 GLN G 113 GLN H 113 GLN I 113 GLN J 113 GLN K 113 GLN L 113 GLN M 113 GLN N 113 GLN O 113 GLN P 113 GLN Q 113 GLN R 113 GLN S 113 GLN T 113 GLN U 113 GLN V 113 GLN W 113 GLN X 113 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34074 Z= 0.211 Angle : 0.546 7.490 45970 Z= 0.316 Chirality : 0.040 0.155 4858 Planarity : 0.003 0.019 6068 Dihedral : 4.183 23.081 4494 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.59 % Allowed : 11.33 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.77 (0.12), residues: 4066 helix: 3.74 (0.08), residues: 3034 sheet: None (None), residues: 0 loop : -1.70 (0.15), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 94 HIS 0.001 0.000 HIS Q 14 PHE 0.009 0.002 PHE A 133 TYR 0.016 0.002 TYR X 40 ARG 0.002 0.000 ARG Q 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 424 time to evaluate : 4.011 Fit side-chains outliers start: 21 outliers final: 18 residues processed: 424 average time/residue: 2.1019 time to fit residues: 1015.7424 Evaluate side-chains 439 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 421 time to evaluate : 3.837 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 1.9683 time to fit residues: 46.0298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 309 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34074 Z= 0.205 Angle : 0.536 6.081 45970 Z= 0.310 Chirality : 0.039 0.134 4858 Planarity : 0.003 0.020 6068 Dihedral : 4.157 23.106 4494 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.65 % Allowed : 11.59 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.90 (0.12), residues: 4066 helix: 3.85 (0.08), residues: 3034 sheet: None (None), residues: 0 loop : -1.70 (0.15), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 94 HIS 0.001 0.000 HIS Q 14 PHE 0.009 0.002 PHE A 133 TYR 0.015 0.002 TYR P 40 ARG 0.002 0.000 ARG U 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 421 time to evaluate : 4.221 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 422 average time/residue: 2.1811 time to fit residues: 1047.9704 Evaluate side-chains 433 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 422 time to evaluate : 4.257 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 2.1454 time to fit residues: 32.9687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.0270 chunk 376 optimal weight: 10.0000 chunk 343 optimal weight: 8.9990 chunk 366 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 287 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 331 optimal weight: 8.9990 chunk 346 optimal weight: 9.9990 chunk 365 optimal weight: 5.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 34074 Z= 0.295 Angle : 0.636 7.971 45970 Z= 0.366 Chirality : 0.044 0.186 4858 Planarity : 0.004 0.035 6068 Dihedral : 4.354 23.604 4494 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.62 % Allowed : 11.64 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.42 (0.12), residues: 4066 helix: 3.42 (0.08), residues: 3058 sheet: None (None), residues: 0 loop : -1.75 (0.15), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 94 HIS 0.002 0.001 HIS G 106 PHE 0.011 0.002 PHE A 133 TYR 0.018 0.002 TYR V 40 ARG 0.003 0.000 ARG W 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 424 time to evaluate : 4.225 Fit side-chains outliers start: 22 outliers final: 0 residues processed: 424 average time/residue: 2.0897 time to fit residues: 1009.3061 Evaluate side-chains 423 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 4.015 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 8.9990 chunk 387 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 20.0000 chunk 406 optimal weight: 10.0000 chunk 374 optimal weight: 9.9990 chunk 323 optimal weight: 0.0970 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN C 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34074 Z= 0.178 Angle : 0.506 7.571 45970 Z= 0.294 Chirality : 0.038 0.133 4858 Planarity : 0.003 0.019 6068 Dihedral : 4.073 22.382 4494 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.71 % Allowed : 11.33 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.08 (0.12), residues: 4066 helix: 3.96 (0.08), residues: 3034 sheet: None (None), residues: 0 loop : -1.58 (0.15), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 94 HIS 0.001 0.000 HIS G 58 PHE 0.009 0.002 PHE A 133 TYR 0.015 0.002 TYR V 40 ARG 0.002 0.000 ARG B 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 420 time to evaluate : 3.951 Fit side-chains outliers start: 25 outliers final: 0 residues processed: 420 average time/residue: 2.1036 time to fit residues: 1007.4145 Evaluate side-chains 417 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 4.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 9.9990 chunk 344 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 324 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.110026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.097185 restraints weight = 85975.651| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.70 r_work: 0.2965 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 34074 Z= 0.323 Angle : 0.661 6.796 45970 Z= 0.379 Chirality : 0.045 0.159 4858 Planarity : 0.004 0.040 6068 Dihedral : 4.388 23.406 4494 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.85 % Allowed : 11.64 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.36 (0.12), residues: 4066 helix: 3.37 (0.08), residues: 3058 sheet: None (None), residues: 0 loop : -1.73 (0.15), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 94 HIS 0.002 0.001 HIS W 61 PHE 0.011 0.003 PHE A 56 TYR 0.018 0.002 TYR V 40 ARG 0.003 0.001 ARG K 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15448.07 seconds wall clock time: 273 minutes 4.49 seconds (16384.49 seconds total)