Starting phenix.real_space_refine (version: dev) on Fri Dec 16 17:16:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k3o_9910/12_2022/6k3o_9910_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k3o_9910/12_2022/6k3o_9910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k3o_9910/12_2022/6k3o_9910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k3o_9910/12_2022/6k3o_9910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k3o_9910/12_2022/6k3o_9910_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k3o_9910/12_2022/6k3o_9910_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 sd= 1.138 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 33": "OD1" <-> "OD2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B ASP 33": "OD1" <-> "OD2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 60": "OD1" <-> "OD2" Residue "B ASP 113": "OD1" <-> "OD2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "C TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 60": "OD1" <-> "OD2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "G TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G ASP 60": "OD1" <-> "OD2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "I ASP 33": "OD1" <-> "OD2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I ASP 60": "OD1" <-> "OD2" Residue "I ASP 113": "OD1" <-> "OD2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I GLU 155": "OE1" <-> "OE2" Residue "J ASP 33": "OD1" <-> "OD2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J ASP 113": "OD1" <-> "OD2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K ASP 33": "OD1" <-> "OD2" Residue "K TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 51": "OE1" <-> "OE2" Residue "K GLU 127": "OE1" <-> "OE2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "L ASP 33": "OD1" <-> "OD2" Residue "L TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L ASP 113": "OD1" <-> "OD2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L ASP 132": "OD1" <-> "OD2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "M PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 33": "OD1" <-> "OD2" Residue "M TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ASP 113": "OD1" <-> "OD2" Residue "M GLU 121": "OE1" <-> "OE2" Residue "N PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 60": "OD1" <-> "OD2" Residue "N ASP 126": "OD1" <-> "OD2" Residue "N GLU 127": "OE1" <-> "OE2" Residue "O ASP 33": "OD1" <-> "OD2" Residue "O TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O GLU 51": "OE1" <-> "OE2" Residue "O GLU 56": "OE1" <-> "OE2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O ASP 113": "OD1" <-> "OD2" Residue "O GLU 121": "OE1" <-> "OE2" Residue "O ASP 126": "OD1" <-> "OD2" Residue "P GLU 18": "OE1" <-> "OE2" Residue "P ASP 33": "OD1" <-> "OD2" Residue "P TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "P GLU 96": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P ASP 132": "OD1" <-> "OD2" Residue "P ASP 139": "OD1" <-> "OD2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "Q GLU 47": "OE1" <-> "OE2" Residue "Q GLU 51": "OE1" <-> "OE2" Residue "Q ASP 60": "OD1" <-> "OD2" Residue "Q ASP 113": "OD1" <-> "OD2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q ASP 132": "OD1" <-> "OD2" Residue "R PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 47": "OE1" <-> "OE2" Residue "R ASP 50": "OD1" <-> "OD2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R ASP 113": "OD1" <-> "OD2" Residue "R GLU 121": "OE1" <-> "OE2" Residue "S ASP 33": "OD1" <-> "OD2" Residue "S TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "S ASP 50": "OD1" <-> "OD2" Residue "S ASP 60": "OD1" <-> "OD2" Residue "S ASP 113": "OD1" <-> "OD2" Residue "S GLU 155": "OE1" <-> "OE2" Residue "T ASP 33": "OD1" <-> "OD2" Residue "T TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 60": "OD1" <-> "OD2" Residue "T GLU 121": "OE1" <-> "OE2" Residue "T ASP 139": "OD1" <-> "OD2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 33": "OD1" <-> "OD2" Residue "U TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U GLU 51": "OE1" <-> "OE2" Residue "U ASP 60": "OD1" <-> "OD2" Residue "U GLU 127": "OE1" <-> "OE2" Residue "U ASP 139": "OD1" <-> "OD2" Residue "U GLU 155": "OE1" <-> "OE2" Residue "V TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ASP 50": "OD1" <-> "OD2" Residue "V ASP 60": "OD1" <-> "OD2" Residue "V GLU 96": "OE1" <-> "OE2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "V GLU 155": "OE1" <-> "OE2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 33": "OD1" <-> "OD2" Residue "W TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 47": "OE1" <-> "OE2" Residue "W ASP 50": "OD1" <-> "OD2" Residue "W ASP 60": "OD1" <-> "OD2" Residue "W GLU 96": "OE1" <-> "OE2" Residue "W ASP 113": "OD1" <-> "OD2" Residue "W GLU 121": "OE1" <-> "OE2" Residue "X ASP 33": "OD1" <-> "OD2" Residue "X TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 47": "OE1" <-> "OE2" Residue "X ASP 60": "OD1" <-> "OD2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "X ASP 113": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 31508 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1301 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "H" 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: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.23, per 1000 atoms: 0.52 Number of scatterers: 31508 At special positions: 0 Unit cell: (132.09, 132.09, 132.09, 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 36 26.01 S 96 16.00 O 6054 8.00 N 5375 7.00 C 19947 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.91 Conformation dependent library (CDL) restraints added in 4.7 seconds 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7292 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 0 sheets defined 78.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 removed outlier: 4.037A pdb=" N LYS A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 64 Processing helix chain 'A' and resid 84 through 111 removed outlier: 4.426A pdb=" N LYS A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 144 Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.226A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 35 removed outlier: 4.104A pdb=" N LYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 64 removed outlier: 3.904A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 111 removed outlier: 4.401A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 144 Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.770A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 35 removed outlier: 4.086A pdb=" N LYS C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 64 Processing helix chain 'C' and resid 83 through 111 removed outlier: 4.395A pdb=" N LYS C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 144 Processing helix chain 'C' and resid 146 through 152 removed outlier: 4.399A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 35 removed outlier: 4.102A pdb=" N LYS D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 64 removed outlier: 3.916A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 111 removed outlier: 4.368A pdb=" N LYS D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 144 Processing helix chain 'D' and resid 146 through 152 removed outlier: 4.394A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 35 removed outlier: 4.064A pdb=" N LYS F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 64 removed outlier: 3.691A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 111 removed outlier: 4.430A pdb=" N LYS F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 144 Processing helix chain 'F' and resid 146 through 152 removed outlier: 4.464A pdb=" N THR F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 removed outlier: 4.092A pdb=" N LYS E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 64 Processing helix chain 'E' and resid 83 through 111 removed outlier: 4.426A pdb=" N LYS E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 144 Processing helix chain 'E' and resid 146 through 152 removed outlier: 4.350A pdb=" N THR E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 removed outlier: 4.101A pdb=" N LYS G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 64 Processing helix chain 'G' and resid 83 through 111 removed outlier: 4.412A pdb=" N LYS G 111 " --> pdb=" O VAL G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 144 Processing helix chain 'G' and resid 146 through 152 removed outlier: 4.398A pdb=" N THR G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 35 removed outlier: 4.085A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 64 Processing helix chain 'H' and resid 83 through 111 removed outlier: 4.419A pdb=" N LYS H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 144 Processing helix chain 'H' and resid 146 through 152 removed outlier: 3.912A pdb=" N THR H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 35 removed outlier: 4.089A pdb=" N LYS I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 64 Processing helix chain 'I' and resid 83 through 111 removed outlier: 4.390A pdb=" N LYS I 111 " --> pdb=" O VAL I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 144 Processing helix chain 'I' and resid 146 through 152 removed outlier: 3.893A pdb=" N THR I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 35 removed outlier: 4.079A pdb=" N LYS J 35 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 64 Processing helix chain 'J' and resid 83 through 111 removed outlier: 4.397A pdb=" N LYS J 111 " --> pdb=" O VAL J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 144 Processing helix chain 'J' and resid 146 through 152 removed outlier: 4.324A pdb=" N THR J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 35 removed outlier: 4.134A pdb=" N LYS K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 64 removed outlier: 3.882A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 4.427A pdb=" N LYS K 111 " --> pdb=" O VAL K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 144 Processing helix chain 'K' and resid 146 through 152 removed outlier: 3.771A pdb=" N THR K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 35 removed outlier: 4.096A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 64 Processing helix chain 'L' and resid 83 through 111 removed outlier: 4.379A pdb=" N LYS L 111 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 144 Processing helix chain 'L' and resid 146 through 152 removed outlier: 4.345A pdb=" N THR L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 35 removed outlier: 4.133A pdb=" N LYS M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 64 removed outlier: 3.927A pdb=" N TYR M 43 " --> pdb=" O LYS M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 111 removed outlier: 4.391A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 144 Processing helix chain 'M' and resid 146 through 152 removed outlier: 4.405A pdb=" N THR M 152 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 35 removed outlier: 3.774A pdb=" N LYS N 35 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 64 Processing helix chain 'N' and resid 83 through 111 removed outlier: 4.407A pdb=" N LYS N 111 " --> pdb=" O VAL N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 144 Processing helix chain 'N' and resid 146 through 152 removed outlier: 4.382A pdb=" N THR N 152 " --> pdb=" O LEU N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 35 removed outlier: 4.079A pdb=" N LYS O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 39 through 64 Processing helix chain 'O' and resid 84 through 111 removed outlier: 4.401A pdb=" N LYS O 111 " --> pdb=" O VAL O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 144 Processing helix chain 'O' and resid 146 through 152 removed outlier: 3.803A pdb=" N THR O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 35 removed outlier: 4.121A pdb=" N LYS P 35 " --> pdb=" O LEU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 64 removed outlier: 3.895A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 111 removed outlier: 4.401A pdb=" N LYS P 111 " --> pdb=" O VAL P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 144 Processing helix chain 'P' and resid 146 through 152 removed outlier: 3.770A pdb=" N THR P 152 " --> pdb=" O LEU P 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 35 removed outlier: 4.080A pdb=" N LYS Q 35 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 64 Processing helix chain 'Q' and resid 83 through 111 removed outlier: 4.394A pdb=" N LYS Q 111 " --> pdb=" O VAL Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 144 Processing helix chain 'Q' and resid 146 through 152 removed outlier: 4.400A pdb=" N THR Q 152 " --> pdb=" O LEU Q 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 35 removed outlier: 4.129A pdb=" N LYS R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 64 removed outlier: 3.918A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 111 removed outlier: 4.421A pdb=" N LYS R 111 " --> pdb=" O VAL R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 144 Processing helix chain 'R' and resid 146 through 152 removed outlier: 4.411A pdb=" N THR R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 35 removed outlier: 4.063A pdb=" N LYS S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 64 removed outlier: 3.718A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 111 removed outlier: 4.446A pdb=" N LYS S 111 " --> pdb=" O VAL S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 144 Processing helix chain 'S' and resid 146 through 152 removed outlier: 4.402A pdb=" N THR S 152 " --> pdb=" O LEU S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 35 removed outlier: 4.031A pdb=" N LYS T 35 " --> pdb=" O LEU T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 64 Processing helix chain 'T' and resid 84 through 111 removed outlier: 4.425A pdb=" N LYS T 111 " --> pdb=" O VAL T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 144 Processing helix chain 'T' and resid 146 through 152 removed outlier: 3.887A pdb=" N THR T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 35 removed outlier: 4.135A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 64 removed outlier: 3.879A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 111 removed outlier: 4.413A pdb=" N LYS U 111 " --> pdb=" O VAL U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 115 through 144 Processing helix chain 'U' and resid 146 through 152 removed outlier: 3.799A pdb=" N THR U 152 " --> pdb=" O LEU U 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 35 removed outlier: 4.064A pdb=" N LYS V 35 " --> pdb=" O LEU V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 39 through 64 Processing helix chain 'V' and resid 83 through 111 removed outlier: 4.394A pdb=" N LYS V 111 " --> pdb=" O VAL V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 115 through 144 Processing helix chain 'V' and resid 146 through 152 removed outlier: 4.409A pdb=" N THR V 152 " --> pdb=" O LEU V 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 35 removed outlier: 4.131A pdb=" N LYS W 35 " --> pdb=" O LEU W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 64 removed outlier: 3.844A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 111 removed outlier: 4.403A pdb=" N LYS W 111 " --> pdb=" O VAL W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 115 through 144 Processing helix chain 'W' and resid 146 through 152 removed outlier: 4.383A pdb=" N THR W 152 " --> pdb=" O LEU W 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 35 removed outlier: 4.108A pdb=" N LYS X 35 " --> pdb=" O LEU X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 64 removed outlier: 3.772A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 111 removed outlier: 4.448A pdb=" N LYS X 111 " --> pdb=" O VAL X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 144 Processing helix chain 'X' and resid 146 through 152 removed outlier: 4.342A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 2395 hydrogen bonds defined for protein. 7185 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: 9.17 Time building geometry restraints manager: 14.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 13390 1.40 - 1.57: 18442 1.57 - 1.75: 0 1.75 - 1.92: 192 1.92 - 2.09: 48 Bond restraints: 32072 Sorted by residual: bond pdb=" CA GLN S 158 " pdb=" C GLN S 158 " ideal model delta sigma weight residual 1.534 1.524 0.010 9.50e-03 1.11e+04 1.17e+00 bond pdb=" CA ALA O 110 " pdb=" C ALA O 110 " ideal model delta sigma weight residual 1.523 1.543 -0.019 1.80e-02 3.09e+03 1.14e+00 bond pdb=" CA GLN N 158 " pdb=" C GLN N 158 " ideal model delta sigma weight residual 1.534 1.524 0.010 9.50e-03 1.11e+04 1.07e+00 bond pdb=" CA ALA P 110 " pdb=" C ALA P 110 " ideal model delta sigma weight residual 1.523 1.542 -0.018 1.80e-02 3.09e+03 1.05e+00 bond pdb=" CA ALA H 110 " pdb=" C ALA H 110 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.80e-02 3.09e+03 1.02e+00 ... (remaining 32067 not shown) Histogram of bond angle deviations from ideal: 86.88 - 105.28: 295 105.28 - 123.69: 42139 123.69 - 142.10: 1042 142.10 - 160.51: 0 160.51 - 178.92: 24 Bond angle restraints: 43500 Sorted by residual: angle pdb=" C ARG A 109 " pdb=" N ALA A 110 " pdb=" CA ALA A 110 " ideal model delta sigma weight residual 122.31 115.44 6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" C ARG E 109 " pdb=" N ALA E 110 " pdb=" CA ALA E 110 " ideal model delta sigma weight residual 122.31 115.47 6.84 2.00e+00 2.50e-01 1.17e+01 angle pdb=" C ARG R 109 " pdb=" N ALA R 110 " pdb=" CA ALA R 110 " ideal model delta sigma weight residual 122.31 115.47 6.84 2.00e+00 2.50e-01 1.17e+01 angle pdb=" C ARG T 109 " pdb=" N ALA T 110 " pdb=" CA ALA T 110 " ideal model delta sigma weight residual 122.31 115.50 6.81 2.00e+00 2.50e-01 1.16e+01 angle pdb=" C ARG W 109 " pdb=" N ALA W 110 " pdb=" CA ALA W 110 " ideal model delta sigma weight residual 122.31 115.51 6.80 2.00e+00 2.50e-01 1.16e+01 ... (remaining 43495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 17020 17.69 - 35.38: 1797 35.38 - 53.07: 270 53.07 - 70.76: 73 70.76 - 88.45: 20 Dihedral angle restraints: 19180 sinusoidal: 8002 harmonic: 11178 Sorted by residual: dihedral pdb=" C2C HEM X 201 " pdb=" C3C HEM X 201 " pdb=" CAC HEM X 201 " pdb=" CBC HEM X 201 " ideal model delta sinusoidal sigma weight residual -0.00 38.65 -38.65 2 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" C2D HEM S 202 " pdb=" C3D HEM S 202 " pdb=" CAD HEM S 202 " pdb=" CBD HEM S 202 " ideal model delta sinusoidal sigma weight residual 180.00 91.55 88.45 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2A HEM F 202 " pdb=" CAA HEM F 202 " pdb=" CBA HEM F 202 " pdb=" CGA HEM F 202 " ideal model delta sinusoidal sigma weight residual 0.00 -86.17 86.17 2 2.00e+01 2.50e-03 1.19e+01 ... (remaining 19177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 2942 0.021 - 0.042: 1100 0.042 - 0.064: 482 0.064 - 0.085: 173 0.085 - 0.106: 132 Chirality restraints: 4829 Sorted by residual: chirality pdb=" CA VAL U 77 " pdb=" N VAL U 77 " pdb=" C VAL U 77 " pdb=" CB VAL U 77 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.82e-01 chirality pdb=" CA VAL J 77 " pdb=" N VAL J 77 " pdb=" C VAL J 77 " pdb=" CB VAL J 77 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.79e-01 chirality pdb=" CA ILE U 154 " pdb=" N ILE U 154 " pdb=" C ILE U 154 " pdb=" CB ILE U 154 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.78e-01 ... (remaining 4826 not shown) Planarity restraints: 5615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 37 " -0.012 2.00e-02 2.50e+03 8.48e-03 1.80e+00 pdb=" CG TRP A 37 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 37 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 37 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 37 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 37 " -0.011 2.00e-02 2.50e+03 7.75e-03 1.50e+00 pdb=" CG TRP O 37 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP O 37 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP O 37 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP O 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP O 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 37 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 37 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP O 37 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP T 37 " 0.011 2.00e-02 2.50e+03 7.72e-03 1.49e+00 pdb=" CG TRP T 37 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP T 37 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP T 37 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP T 37 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP T 37 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP T 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 37 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 37 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP T 37 " 0.001 2.00e-02 2.50e+03 ... (remaining 5612 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 24 1.84 - 2.61: 553 2.61 - 3.37: 44168 3.37 - 4.14: 64356 4.14 - 4.90: 124963 Nonbonded interactions: 234064 Sorted by model distance: nonbonded pdb=" OE2 GLU O 127 " pdb="FE FE2 O 201 " model vdw 1.077 3.000 nonbonded pdb=" OE1 GLU K 18 " pdb=" OE1 GLU K 51 " model vdw 1.308 3.040 nonbonded pdb=" OE1 GLU M 18 " pdb=" OE1 GLU M 51 " model vdw 1.322 3.040 nonbonded pdb=" OE1 GLU U 18 " pdb=" OE1 GLU U 51 " model vdw 1.335 3.040 nonbonded pdb=" OE1 GLU S 18 " pdb=" OE1 GLU S 51 " model vdw 1.342 3.040 ... (remaining 234059 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 1 through 157) selection = (chain 'B' and resid 1 through 157) selection = (chain 'C' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'D' and resid 1 through 157) selection = (chain 'E' and resid 1 through 157) selection = (chain 'F' and resid 1 through 157) selection = (chain 'G' and resid 1 through 157) selection = (chain 'H' and resid 1 through 157) selection = (chain 'I' and resid 1 through 157) selection = (chain 'J' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'K' and resid 1 through 157) selection = (chain 'L' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'M' and resid 1 through 157) selection = (chain 'N' and resid 1 through 157) selection = (chain 'O' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'P' and resid 1 through 157) selection = (chain 'Q' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'R' and resid 1 through 157) selection = (chain 'S' and resid 1 through 157) selection = (chain 'T' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'U' and resid 1 through 157) selection = (chain 'V' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'W' and resid 1 through 157) selection = (chain 'X' and resid 1 through 157) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 36 7.16 5 S 96 5.16 5 C 19947 2.51 5 N 5375 2.21 5 O 6054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.300 Check model and map are aligned: 0.490 Convert atoms to be neutral: 0.310 Process input model: 76.030 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 : 0.003 0.060 32072 Z= 0.220 Angle : 0.557 9.174 43500 Z= 0.325 Chirality : 0.031 0.106 4829 Planarity : 0.002 0.024 5615 Dihedral : 14.463 88.447 11888 Min Nonbonded Distance : 1.077 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.11), residues: 3742 helix: 0.08 (0.08), residues: 2922 sheet: None (None), residues: 0 loop : -4.98 (0.11), residues: 820 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 3.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.3879 time to fit residues: 358.4424 Evaluate side-chains 463 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 3.840 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 6.9990 chunk 272 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 326 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 156 GLN C 24 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN F 24 GLN F 118 ASN F 156 GLN E 24 GLN E 130 HIS G 24 GLN G 130 HIS H 24 GLN I 24 GLN J 24 GLN K 24 GLN ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN M 24 GLN M 156 GLN N 24 GLN N 118 ASN N 130 HIS N 156 GLN O 24 GLN P 24 GLN P 130 HIS P 156 GLN Q 24 GLN Q 130 HIS R 24 GLN S 24 GLN S 118 ASN S 156 GLN T 24 GLN ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 GLN X 24 GLN X 118 ASN X 156 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 32072 Z= 0.246 Angle : 0.655 23.606 43500 Z= 0.305 Chirality : 0.035 0.133 4829 Planarity : 0.003 0.018 5615 Dihedral : 6.435 89.037 4222 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.13), residues: 3742 helix: 2.81 (0.09), residues: 2880 sheet: None (None), residues: 0 loop : -3.36 (0.18), residues: 862 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 593 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 54 residues processed: 602 average time/residue: 0.4114 time to fit residues: 411.5192 Evaluate side-chains 572 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 518 time to evaluate : 3.890 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.2811 time to fit residues: 34.5149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 2.9990 chunk 353 optimal weight: 5.9990 chunk 291 optimal weight: 0.7980 chunk 324 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS G 130 HIS ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 HIS ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN N 130 HIS P 130 HIS Q 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 24 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 32072 Z= 0.261 Angle : 0.615 21.928 43500 Z= 0.295 Chirality : 0.034 0.140 4829 Planarity : 0.003 0.032 5615 Dihedral : 6.649 89.031 4222 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.14), residues: 3742 helix: 3.39 (0.08), residues: 2860 sheet: None (None), residues: 0 loop : -2.80 (0.21), residues: 882 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 531 time to evaluate : 4.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 540 average time/residue: 0.4203 time to fit residues: 372.1214 Evaluate side-chains 520 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 507 time to evaluate : 3.976 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2838 time to fit residues: 12.7241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 156 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 328 optimal weight: 8.9990 chunk 347 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 311 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 HIS J 130 HIS ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS O 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 32072 Z= 0.175 Angle : 0.548 13.719 43500 Z= 0.267 Chirality : 0.032 0.140 4829 Planarity : 0.002 0.025 5615 Dihedral : 6.806 88.811 4222 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.14), residues: 3742 helix: 3.88 (0.08), residues: 2860 sheet: None (None), residues: 0 loop : -2.38 (0.22), residues: 882 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 488 time to evaluate : 3.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 514 average time/residue: 0.3715 time to fit residues: 318.2529 Evaluate side-chains 487 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 461 time to evaluate : 3.881 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2776 time to fit residues: 18.9639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 312 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN B 156 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS G 130 HIS ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 130 HIS ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 130 HIS V 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 32072 Z= 0.259 Angle : 0.619 22.110 43500 Z= 0.288 Chirality : 0.033 0.159 4829 Planarity : 0.003 0.023 5615 Dihedral : 6.765 86.552 4222 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.14), residues: 3742 helix: 3.65 (0.08), residues: 2884 sheet: None (None), residues: 0 loop : -2.45 (0.22), residues: 858 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 538 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 56 residues processed: 582 average time/residue: 0.4075 time to fit residues: 384.7577 Evaluate side-chains 549 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 493 time to evaluate : 3.831 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.2746 time to fit residues: 34.7431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 5.9990 chunk 313 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 348 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS D 130 HIS E 130 HIS ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 32072 Z= 0.298 Angle : 0.664 20.975 43500 Z= 0.309 Chirality : 0.035 0.164 4829 Planarity : 0.003 0.023 5615 Dihedral : 6.812 88.322 4222 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.14), residues: 3742 helix: 3.58 (0.08), residues: 2891 sheet: None (None), residues: 0 loop : -2.37 (0.22), residues: 851 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 493 time to evaluate : 3.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 61 residues processed: 546 average time/residue: 0.3985 time to fit residues: 355.1912 Evaluate side-chains 522 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 461 time to evaluate : 3.765 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 61 outliers final: 1 residues processed: 61 average time/residue: 0.2954 time to fit residues: 37.7239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN L 130 HIS ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 54 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 32072 Z= 0.214 Angle : 0.599 22.767 43500 Z= 0.286 Chirality : 0.033 0.214 4829 Planarity : 0.002 0.020 5615 Dihedral : 6.803 89.582 4222 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.14), residues: 3742 helix: 3.95 (0.08), residues: 2876 sheet: None (None), residues: 0 loop : -2.20 (0.23), residues: 866 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 499 time to evaluate : 3.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 6 residues processed: 513 average time/residue: 0.3873 time to fit residues: 327.9096 Evaluate side-chains 475 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 469 time to evaluate : 3.892 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.4375 time to fit residues: 9.3321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 272 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 HIS K 130 HIS K 156 GLN ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 130 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 32072 Z= 0.303 Angle : 0.668 24.006 43500 Z= 0.314 Chirality : 0.035 0.172 4829 Planarity : 0.003 0.022 5615 Dihedral : 6.818 89.309 4222 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.13), residues: 3742 helix: 3.60 (0.08), residues: 2891 sheet: None (None), residues: 0 loop : -2.28 (0.23), residues: 851 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 478 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 53 residues processed: 529 average time/residue: 0.4081 time to fit residues: 351.8483 Evaluate side-chains 534 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 481 time to evaluate : 4.112 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 53 outliers final: 1 residues processed: 53 average time/residue: 0.3113 time to fit residues: 35.0217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 303 optimal weight: 1.9990 chunk 323 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 292 optimal weight: 4.9990 chunk 305 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS D 130 HIS ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 HIS ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 32072 Z= 0.256 Angle : 0.658 24.896 43500 Z= 0.307 Chirality : 0.033 0.154 4829 Planarity : 0.003 0.024 5615 Dihedral : 6.797 88.947 4222 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.14), residues: 3742 helix: 3.71 (0.08), residues: 2900 sheet: None (None), residues: 0 loop : -2.28 (0.23), residues: 842 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 497 time to evaluate : 3.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 505 average time/residue: 0.3966 time to fit residues: 326.3975 Evaluate side-chains 470 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 463 time to evaluate : 3.562 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.3515 time to fit residues: 8.8639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 6.9990 chunk 341 optimal weight: 9.9990 chunk 208 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 358 optimal weight: 0.9990 chunk 330 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS D 130 HIS ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 32072 Z= 0.223 Angle : 0.655 25.344 43500 Z= 0.301 Chirality : 0.033 0.164 4829 Planarity : 0.003 0.025 5615 Dihedral : 6.668 87.751 4222 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.12 (0.14), residues: 3742 helix: 3.95 (0.08), residues: 2885 sheet: None (None), residues: 0 loop : -2.11 (0.23), residues: 857 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 491 time to evaluate : 4.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 493 average time/residue: 0.4040 time to fit residues: 326.8197 Evaluate side-chains 478 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 470 time to evaluate : 4.258 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.3490 time to fit residues: 10.2056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 3.9990 chunk 304 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 263 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS D 130 HIS ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 HIS ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.144501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129744 restraints weight = 46682.014| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.75 r_work: 0.3584 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 32072 Z= 0.276 Angle : 0.699 25.687 43500 Z= 0.317 Chirality : 0.034 0.191 4829 Planarity : 0.003 0.040 5615 Dihedral : 6.741 86.281 4222 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.13), residues: 3742 helix: 3.72 (0.08), residues: 2900 sheet: None (None), residues: 0 loop : -2.21 (0.23), residues: 842 =============================================================================== Job complete usr+sys time: 6369.09 seconds wall clock time: 116 minutes 5.20 seconds (6965.20 seconds total)