Starting phenix.real_space_refine (version: dev) on Tue Feb 28 01:05:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k3o_9910/02_2023/6k3o_9910_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k3o_9910/02_2023/6k3o_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_9910/02_2023/6k3o_9910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k3o_9910/02_2023/6k3o_9910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k3o_9910/02_2023/6k3o_9910_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k3o_9910/02_2023/6k3o_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 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-4877/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: 17.07, per 1000 atoms: 0.54 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: 13.90 Conformation dependent library (CDL) restraints added in 4.4 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: 1.62 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: 10.11 Time building geometry restraints manager: 14.31 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: 1.070 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: 6.550 Check model and map are aligned: 0.490 Process input model: 77.050 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.260 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.230 ------------------------------------------------------------------------------- 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 : 3.542 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: 0.4038 time to fit residues: 370.9097 Evaluate side-chains 463 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 4.421 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1598 ------------------------------------------------------------------------------- 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 23.605 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 : 6.88 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 : 3.647 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: 0.3981 time to fit residues: 394.0399 Evaluate side-chains 572 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 518 time to evaluate : 3.627 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.2637 time to fit residues: 32.6196 ------------------------------------------------------------------------------- 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: 6.9990 chunk 272 optimal weight: 0.9990 chunk 222 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 2.9990 chunk 353 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 324 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8221 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 0.067 32072 Z= 0.253 Angle : 0.611 21.675 43500 Z= 0.292 Chirality : 0.034 0.141 4829 Planarity : 0.003 0.029 5615 Dihedral : 6.657 89.127 4222 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.51 % 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: 3.19 (0.14), residues: 3742 helix: 3.42 (0.08), residues: 2860 sheet: None (None), residues: 0 loop : -2.78 (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 551 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 534 time to evaluate : 3.636 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: 17 outliers final: 11 residues processed: 541 average time/residue: 0.4142 time to fit residues: 363.9839 Evaluate side-chains 521 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 510 time to evaluate : 3.906 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2784 time to fit residues: 11.6286 ------------------------------------------------------------------------------- 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: 1.9990 chunk 246 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 156 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 328 optimal weight: 8.9990 chunk 347 optimal weight: 0.9980 chunk 171 optimal weight: 7.9990 chunk 311 optimal weight: 8.9990 chunk 93 optimal weight: 0.0370 overall best weight: 1.5062 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 HIS ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS O 130 HIS ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8153 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 32072 Z= 0.197 Angle : 0.557 15.057 43500 Z= 0.270 Chirality : 0.032 0.139 4829 Planarity : 0.002 0.019 5615 Dihedral : 6.743 89.019 4222 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 1.17 % 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: 3.73 (0.14), residues: 3742 helix: 3.77 (0.08), residues: 2860 sheet: None (None), residues: 0 loop : -2.43 (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 581 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 542 time to evaluate : 3.660 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: 39 outliers final: 26 residues processed: 548 average time/residue: 0.3923 time to fit residues: 356.8810 Evaluate side-chains 532 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 506 time to evaluate : 3.491 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2638 time to fit residues: 17.8871 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 296 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 312 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS P 130 HIS 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 32072 Z= 0.292 Angle : 0.625 22.298 43500 Z= 0.297 Chirality : 0.034 0.139 4829 Planarity : 0.003 0.020 5615 Dihedral : 6.756 87.575 4222 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 3.22 % 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: 3.44 (0.14), residues: 3742 helix: 3.51 (0.08), residues: 2878 sheet: None (None), residues: 0 loop : -2.46 (0.22), residues: 864 *********************** 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 651 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 544 time to evaluate : 3.787 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 revert: symmetry clash outliers start: 107 outliers final: 73 residues processed: 602 average time/residue: 0.4341 time to fit residues: 423.2066 Evaluate side-chains 574 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 501 time to evaluate : 4.186 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.2895 time to fit residues: 45.6789 ------------------------------------------------------------------------------- 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: 6.9990 chunk 313 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 348 optimal weight: 0.0770 chunk 289 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 32072 Z= 0.237 Angle : 0.616 18.957 43500 Z= 0.290 Chirality : 0.033 0.174 4829 Planarity : 0.002 0.017 5615 Dihedral : 6.810 87.919 4222 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 1.96 % 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: 3.77 (0.14), residues: 3742 helix: 3.78 (0.08), residues: 2866 sheet: None (None), residues: 0 loop : -2.39 (0.22), residues: 876 *********************** 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 566 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 501 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: 65 outliers final: 39 residues processed: 529 average time/residue: 0.4093 time to fit residues: 352.5872 Evaluate side-chains 519 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 480 time to evaluate : 3.956 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3207 time to fit residues: 29.3476 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 2.9990 chunk 198 optimal weight: 0.3980 chunk 254 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 293 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 346 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 32072 Z= 0.208 Angle : 0.590 22.253 43500 Z= 0.282 Chirality : 0.032 0.145 4829 Planarity : 0.003 0.040 5615 Dihedral : 6.800 85.452 4222 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 1.05 % 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: 3.97 (0.14), residues: 3742 helix: 3.88 (0.08), residues: 2875 sheet: None (None), residues: 0 loop : -2.21 (0.23), residues: 867 *********************** 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 544 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 509 time to evaluate : 3.790 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: 35 outliers final: 15 residues processed: 517 average time/residue: 0.4162 time to fit residues: 353.2547 Evaluate side-chains 494 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 479 time to evaluate : 3.643 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2933 time to fit residues: 13.2040 ------------------------------------------------------------------------------- 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: 1.9990 chunk 138 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 272 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN M 130 HIS N 130 HIS P 130 HIS Q 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 130 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 32072 Z= 0.338 Angle : 0.683 24.721 43500 Z= 0.323 Chirality : 0.035 0.161 4829 Planarity : 0.003 0.019 5615 Dihedral : 6.830 89.583 4222 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 2.98 % 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: 3.43 (0.13), residues: 3742 helix: 3.42 (0.08), residues: 2890 sheet: None (None), residues: 0 loop : -2.24 (0.23), residues: 852 *********************** 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 577 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 478 time to evaluate : 3.755 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: 99 outliers final: 74 residues processed: 524 average time/residue: 0.4339 time to fit residues: 367.1005 Evaluate side-chains 548 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 474 time to evaluate : 3.554 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.2971 time to fit residues: 46.2694 ------------------------------------------------------------------------------- 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: 0.0030 chunk 332 optimal weight: 4.9990 chunk 303 optimal weight: 6.9990 chunk 323 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 292 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 322 optimal weight: 5.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 HIS M 130 HIS ** 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: 0.8161 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 32072 Z= 0.208 Angle : 0.620 25.104 43500 Z= 0.297 Chirality : 0.033 0.166 4829 Planarity : 0.002 0.020 5615 Dihedral : 6.908 89.599 4222 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.45 % 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: 4.09 (0.14), residues: 3742 helix: 3.93 (0.08), residues: 2872 sheet: None (None), residues: 0 loop : -1.99 (0.23), residues: 870 *********************** 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 517 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 502 time to evaluate : 3.518 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: 15 outliers final: 1 residues processed: 507 average time/residue: 0.4168 time to fit residues: 347.2946 Evaluate side-chains 473 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 472 time to evaluate : 3.731 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6613 time to fit residues: 6.0030 ------------------------------------------------------------------------------- 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: 6.9990 chunk 208 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 330 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 220 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS ** 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** ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 32072 Z= 0.250 Angle : 0.655 26.230 43500 Z= 0.306 Chirality : 0.033 0.179 4829 Planarity : 0.003 0.051 5615 Dihedral : 6.763 89.458 4222 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 3.92 (0.14), residues: 3742 helix: 3.78 (0.08), residues: 2899 sheet: None (None), residues: 0 loop : -2.17 (0.23), residues: 843 ********************** 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 513 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 480 time to evaluate : 4.256 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: 33 outliers final: 23 residues processed: 483 average time/residue: 0.4403 time to fit residues: 349.0759 Evaluate side-chains 500 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 477 time to evaluate : 3.891 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.3014 time to fit residues: 18.5881 ------------------------------------------------------------------------------- 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: 2.9990 chunk 87 optimal weight: 10.0000 chunk 263 optimal weight: 0.0050 chunk 42 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 N 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 ** 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 = 0.4016 r_free = 0.4016 target = 0.152260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138619 restraints weight = 46375.593| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.54 r_work: 0.3709 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.093 32072 Z= 0.248 Angle : 0.661 26.230 43500 Z= 0.307 Chirality : 0.033 0.170 4829 Planarity : 0.003 0.026 5615 Dihedral : 6.676 88.863 4222 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 4.00 (0.14), residues: 3742 helix: 3.84 (0.08), residues: 2899 sheet: None (None), residues: 0 loop : -2.15 (0.23), residues: 843 =============================================================================== Job complete usr+sys time: 6505.95 seconds wall clock time: 119 minutes 22.47 seconds (7162.47 seconds total)