Starting phenix.real_space_refine on Thu Mar 21 23:30:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6p_33645/03_2024/7y6p_33645_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6p_33645/03_2024/7y6p_33645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6p_33645/03_2024/7y6p_33645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6p_33645/03_2024/7y6p_33645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6p_33645/03_2024/7y6p_33645_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6p_33645/03_2024/7y6p_33645_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 60 7.16 5 S 96 5.16 5 C 19886 2.51 5 N 5356 2.21 5 O 6030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 33": "OD1" <-> "OD2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E ASP 139": "OD1" <-> "OD2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "F ASP 33": "OD1" <-> "OD2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 99": "OD1" <-> "OD2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "H ASP 99": "OD1" <-> "OD2" Residue "I ASP 50": "OD1" <-> "OD2" Residue "I ASP 66": "OD1" <-> "OD2" Residue "I GLU 96": "OE1" <-> "OE2" Residue "I GLU 106": "OE1" <-> "OE2" Residue "I ASP 132": "OD1" <-> "OD2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I GLU 155": "OE1" <-> "OE2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K GLU 128": "OE1" <-> "OE2" Residue "K ASP 139": "OD1" <-> "OD2" Residue "L ASP 33": "OD1" <-> "OD2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L ASP 66": "OD1" <-> "OD2" Residue "L ASP 99": "OD1" <-> "OD2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "M ASP 50": "OD1" <-> "OD2" Residue "M ASP 66": "OD1" <-> "OD2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M ASP 99": "OD1" <-> "OD2" Residue "M ASP 139": "OD1" <-> "OD2" Residue "M GLU 142": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "N ASP 33": "OD1" <-> "OD2" Residue "N ASP 60": "OD1" <-> "OD2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ASP 99": "OD1" <-> "OD2" Residue "N GLU 106": "OE1" <-> "OE2" Residue "N ASP 126": "OD1" <-> "OD2" Residue "N ASP 132": "OD1" <-> "OD2" Residue "N GLU 146": "OE1" <-> "OE2" Residue "O ASP 50": "OD1" <-> "OD2" Residue "O GLU 51": "OE1" <-> "OE2" Residue "O ASP 66": "OD1" <-> "OD2" Residue "O GLU 96": "OE1" <-> "OE2" Residue "O GLU 106": "OE1" <-> "OE2" Residue "O PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 126": "OD1" <-> "OD2" Residue "O GLU 142": "OE1" <-> "OE2" Residue "P ASP 50": "OD1" <-> "OD2" Residue "P GLU 96": "OE1" <-> "OE2" Residue "P ASP 126": "OD1" <-> "OD2" Residue "R TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R ASP 139": "OD1" <-> "OD2" Residue "S ASP 33": "OD1" <-> "OD2" Residue "S ASP 99": "OD1" <-> "OD2" Residue "S GLU 106": "OE1" <-> "OE2" Residue "S GLU 155": "OE1" <-> "OE2" Residue "T ASP 50": "OD1" <-> "OD2" Residue "T GLU 96": "OE1" <-> "OE2" Residue "T ASP 99": "OD1" <-> "OD2" Residue "T GLU 106": "OE1" <-> "OE2" Residue "T ASP 132": "OD1" <-> "OD2" Residue "U ASP 66": "OD1" <-> "OD2" Residue "U ASP 99": "OD1" <-> "OD2" Residue "V ASP 50": "OD1" <-> "OD2" Residue "V GLU 96": "OE1" <-> "OE2" Residue "V ASP 99": "OD1" <-> "OD2" Residue "V GLU 142": "OE1" <-> "OE2" Residue "V GLU 155": "OE1" <-> "OE2" Residue "W ASP 60": "OD1" <-> "OD2" Residue "W ASP 66": "OD1" <-> "OD2" Residue "W GLU 96": "OE1" <-> "OE2" Residue "W ASP 99": "OD1" <-> "OD2" Residue "W GLU 106": "OE1" <-> "OE2" Residue "W GLU 128": "OE1" <-> "OE2" Residue "W ASP 139": "OD1" <-> "OD2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "X ASP 99": "OD1" <-> "OD2" Residue "X GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31428 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: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1280 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} 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: "E" 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: 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: "G" 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: "H" 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: "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: 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: "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: 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: "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: 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: "O" 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: "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: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} 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: 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: "T" 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: "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: 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: "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: 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: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.74, per 1000 atoms: 0.50 Number of scatterers: 31428 At special positions: 0 Unit cell: (131.274, 131.274, 131.274, 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 60 26.01 S 96 16.00 O 6030 8.00 N 5356 7.00 C 19886 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=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.64 Conformation dependent library (CDL) restraints added in 5.5 seconds 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 removed outlier: 3.504A pdb=" N LYS A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 65 removed outlier: 3.527A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 111 removed outlier: 3.623A pdb=" N LYS A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 144 Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.283A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 35 removed outlier: 3.516A pdb=" N LYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 65 removed outlier: 3.830A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 111 removed outlier: 3.634A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 144 Processing helix chain 'B' and resid 146 through 152 removed outlier: 4.235A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 35 Processing helix chain 'C' and resid 38 through 65 removed outlier: 3.527A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 111 removed outlier: 3.624A pdb=" N LYS C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 144 Processing helix chain 'C' and resid 146 through 152 removed outlier: 4.263A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 35 removed outlier: 3.511A pdb=" N LYS D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 65 removed outlier: 3.710A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 111 removed outlier: 3.607A 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: 4.159A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 removed outlier: 3.505A pdb=" N LYS E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 65 removed outlier: 3.520A pdb=" N LEU E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 111 removed outlier: 3.633A pdb=" N LYS E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 144 Processing helix chain 'E' and resid 146 through 152 removed outlier: 4.224A pdb=" N THR E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 35 removed outlier: 3.500A pdb=" N LYS F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 65 removed outlier: 3.670A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 111 removed outlier: 3.637A pdb=" N LYS F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 144 Processing helix chain 'F' and resid 146 through 152 removed outlier: 4.210A pdb=" N THR F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 Processing helix chain 'G' and resid 38 through 65 removed outlier: 3.526A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 111 removed outlier: 3.612A pdb=" N LYS G 111 " --> pdb=" O VAL G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 144 Processing helix chain 'G' and resid 146 through 152 removed outlier: 4.233A pdb=" N THR G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 35 removed outlier: 3.511A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 65 removed outlier: 3.510A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 111 removed outlier: 3.627A pdb=" N LYS H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 144 Processing helix chain 'H' and resid 146 through 152 removed outlier: 4.219A pdb=" N THR H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 35 removed outlier: 3.510A pdb=" N LYS I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 65 removed outlier: 3.525A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 111 removed outlier: 3.628A pdb=" N LYS I 111 " --> pdb=" O VAL I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 144 Processing helix chain 'I' and resid 146 through 152 removed outlier: 4.203A pdb=" N THR I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 35 Processing helix chain 'J' and resid 38 through 65 removed outlier: 3.540A pdb=" N LEU J 65 " --> pdb=" O ARG J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 111 removed outlier: 3.605A pdb=" N LYS J 111 " --> pdb=" O VAL J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 144 Processing helix chain 'J' and resid 146 through 152 removed outlier: 4.279A pdb=" N THR J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 35 removed outlier: 3.516A pdb=" N LYS K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 65 removed outlier: 3.816A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.625A pdb=" N LYS K 111 " --> pdb=" O VAL K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 144 Processing helix chain 'K' and resid 146 through 152 removed outlier: 4.241A pdb=" N THR K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 35 Processing helix chain 'L' and resid 38 through 65 removed outlier: 3.556A pdb=" N GLU L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU L 65 " --> pdb=" O ARG L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 111 removed outlier: 3.570A pdb=" N LYS L 111 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 144 Processing helix chain 'L' and resid 146 through 152 removed outlier: 4.330A pdb=" N THR L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 35 Processing helix chain 'M' and resid 38 through 65 Processing helix chain 'M' and resid 83 through 111 removed outlier: 3.591A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 144 removed outlier: 3.827A pdb=" N ASP M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 152 removed outlier: 4.249A pdb=" N THR M 152 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 35 removed outlier: 3.507A pdb=" N LYS N 35 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 65 removed outlier: 3.519A pdb=" N LEU N 65 " --> pdb=" O ARG N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 111 removed outlier: 3.634A pdb=" N LYS N 111 " --> pdb=" O VAL N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 144 Processing helix chain 'N' and resid 146 through 152 removed outlier: 4.274A pdb=" N THR N 152 " --> pdb=" O LEU N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 35 Processing helix chain 'O' and resid 38 through 65 Processing helix chain 'O' and resid 83 through 111 removed outlier: 3.627A pdb=" N LYS O 111 " --> pdb=" O VAL O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 144 Processing helix chain 'O' and resid 146 through 152 removed outlier: 4.147A pdb=" N THR O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 35 Processing helix chain 'P' and resid 38 through 65 removed outlier: 3.827A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 111 removed outlier: 3.631A pdb=" N LYS P 111 " --> pdb=" O VAL P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 144 Processing helix chain 'P' and resid 146 through 152 removed outlier: 4.193A pdb=" N THR P 152 " --> pdb=" O LEU P 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 35 Processing helix chain 'Q' and resid 38 through 65 removed outlier: 3.527A pdb=" N LEU Q 65 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 111 removed outlier: 3.597A pdb=" N LYS Q 111 " --> pdb=" O VAL Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 144 Processing helix chain 'Q' and resid 146 through 152 removed outlier: 4.258A pdb=" N THR Q 152 " --> pdb=" O LEU Q 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 35 Processing helix chain 'R' and resid 38 through 65 removed outlier: 3.728A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 111 removed outlier: 3.632A pdb=" N LYS R 111 " --> pdb=" O VAL R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 144 Processing helix chain 'R' and resid 146 through 152 removed outlier: 4.190A pdb=" N THR R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 35 removed outlier: 3.507A pdb=" N LYS S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 65 removed outlier: 3.693A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU S 65 " --> pdb=" O ARG S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 111 removed outlier: 3.635A pdb=" N LYS S 111 " --> pdb=" O VAL S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 144 Processing helix chain 'S' and resid 146 through 152 removed outlier: 4.235A pdb=" N THR S 152 " --> pdb=" O LEU S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 35 removed outlier: 3.503A pdb=" N LYS T 35 " --> pdb=" O LEU T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 65 removed outlier: 3.525A pdb=" N LEU T 65 " --> pdb=" O ARG T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 111 removed outlier: 3.635A pdb=" N LYS T 111 " --> pdb=" O VAL T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 144 Processing helix chain 'T' and resid 146 through 152 removed outlier: 4.243A pdb=" N THR T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 35 removed outlier: 3.557A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 65 removed outlier: 3.826A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 111 removed outlier: 3.628A pdb=" N LYS U 111 " --> pdb=" O VAL U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 144 Processing helix chain 'U' and resid 146 through 152 removed outlier: 4.270A pdb=" N THR U 152 " --> pdb=" O LEU U 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 35 Processing helix chain 'V' and resid 38 through 65 Processing helix chain 'V' and resid 83 through 111 removed outlier: 3.601A pdb=" N LYS V 111 " --> pdb=" O VAL V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 114 through 144 removed outlier: 3.811A pdb=" N ASP V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 152 removed outlier: 4.318A pdb=" N THR V 152 " --> pdb=" O LEU V 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 35 Processing helix chain 'W' and resid 38 through 65 removed outlier: 3.855A pdb=" N LYS W 42 " --> pdb=" O THR W 38 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU W 65 " --> pdb=" O ARG W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 111 removed outlier: 3.631A pdb=" N LYS W 111 " --> pdb=" O VAL W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 114 through 144 Processing helix chain 'W' and resid 146 through 152 removed outlier: 4.197A pdb=" N THR W 152 " --> pdb=" O LEU W 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 35 removed outlier: 3.512A pdb=" N LYS X 35 " --> pdb=" O LEU X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 65 removed outlier: 3.712A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU X 65 " --> pdb=" O ARG X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 111 removed outlier: 3.642A pdb=" N LYS X 111 " --> pdb=" O VAL X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 144 Processing helix chain 'X' and resid 146 through 152 removed outlier: 4.246A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 2442 hydrogen bonds defined for protein. 7326 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: 9.40 Time building geometry restraints manager: 14.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 13355 1.40 - 1.58: 18373 1.58 - 1.76: 1 1.76 - 1.94: 191 1.94 - 2.12: 48 Bond restraints: 31968 Sorted by residual: bond pdb=" CB MET N 52 " pdb=" CG MET N 52 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.22e+00 bond pdb=" CG MET F 52 " pdb=" SD MET F 52 " ideal model delta sigma weight residual 1.803 1.763 0.040 2.50e-02 1.60e+03 2.51e+00 bond pdb=" CGA HEM C 203 " pdb=" O2A HEM C 203 " ideal model delta sigma weight residual 1.258 1.289 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" CB MET C 52 " pdb=" CG MET C 52 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.15e+00 bond pdb=" NA HEM F 203 " pdb="FE HEM F 203 " ideal model delta sigma weight residual 2.080 1.990 0.090 7.00e-02 2.04e+02 1.66e+00 ... (remaining 31963 not shown) Histogram of bond angle deviations from ideal: 85.01 - 103.87: 240 103.87 - 122.72: 40596 122.72 - 141.58: 2494 141.58 - 160.43: 1 160.43 - 179.29: 23 Bond angle restraints: 43354 Sorted by residual: angle pdb=" CB MET X 52 " pdb=" CG MET X 52 " pdb=" SD MET X 52 " ideal model delta sigma weight residual 112.70 86.88 25.82 3.00e+00 1.11e-01 7.41e+01 angle pdb=" CA MET F 52 " pdb=" CB MET F 52 " pdb=" CG MET F 52 " ideal model delta sigma weight residual 114.10 127.35 -13.25 2.00e+00 2.50e-01 4.39e+01 angle pdb=" CB MET Q 52 " pdb=" CG MET Q 52 " pdb=" SD MET Q 52 " ideal model delta sigma weight residual 112.70 93.53 19.17 3.00e+00 1.11e-01 4.08e+01 angle pdb=" CB MET C 52 " pdb=" CG MET C 52 " pdb=" SD MET C 52 " ideal model delta sigma weight residual 112.70 94.86 17.84 3.00e+00 1.11e-01 3.54e+01 angle pdb=" CB MET S 52 " pdb=" CG MET S 52 " pdb=" SD MET S 52 " ideal model delta sigma weight residual 112.70 97.53 15.17 3.00e+00 1.11e-01 2.56e+01 ... (remaining 43349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 16841 17.87 - 35.75: 1820 35.75 - 53.62: 326 53.62 - 71.49: 101 71.49 - 89.37: 30 Dihedral angle restraints: 19118 sinusoidal: 7994 harmonic: 11124 Sorted by residual: dihedral pdb=" CA GLU F 51 " pdb=" C GLU F 51 " pdb=" N MET F 52 " pdb=" CA MET F 52 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" C2D HEM F 203 " pdb=" C3D HEM F 203 " pdb=" CAD HEM F 203 " pdb=" CBD HEM F 203 " ideal model delta sinusoidal sigma weight residual 180.00 91.69 88.31 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C1A HEM F 203 " pdb=" C2A HEM F 203 " pdb=" CAA HEM F 203 " pdb=" CBA HEM F 203 " ideal model delta sinusoidal sigma weight residual 180.00 96.11 83.89 2 2.00e+01 2.50e-03 1.19e+01 ... (remaining 19115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4443 0.060 - 0.120: 337 0.120 - 0.181: 25 0.181 - 0.241: 0 0.241 - 0.301: 1 Chirality restraints: 4806 Sorted by residual: chirality pdb=" CA MET Q 52 " pdb=" N MET Q 52 " pdb=" C MET Q 52 " pdb=" CB MET Q 52 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CG LEU P 19 " pdb=" CB LEU P 19 " pdb=" CD1 LEU P 19 " pdb=" CD2 LEU P 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA PHE M 120 " pdb=" N PHE M 120 " pdb=" C PHE M 120 " pdb=" CB PHE M 120 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 4803 not shown) Planarity restraints: 5596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEM F 203 " 0.003 2.00e-02 2.50e+03 2.04e-02 9.35e+00 pdb=" C2A HEM F 203 " 0.002 2.00e-02 2.50e+03 pdb=" C3A HEM F 203 " 0.003 2.00e-02 2.50e+03 pdb=" C4A HEM F 203 " -0.051 2.00e-02 2.50e+03 pdb=" CAA HEM F 203 " -0.004 2.00e-02 2.50e+03 pdb=" CHA HEM F 203 " 0.012 2.00e-02 2.50e+03 pdb=" CHB HEM F 203 " 0.029 2.00e-02 2.50e+03 pdb=" CMA HEM F 203 " 0.007 2.00e-02 2.50e+03 pdb=" NA HEM F 203 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 71 " 0.015 2.00e-02 2.50e+03 2.00e-02 8.00e+00 pdb=" CG TYR T 71 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR T 71 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR T 71 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR T 71 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR T 71 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR T 71 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR T 71 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE V 120 " 0.024 2.00e-02 2.50e+03 2.10e-02 7.70e+00 pdb=" CG PHE V 120 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE V 120 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE V 120 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE V 120 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE V 120 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE V 120 " 0.004 2.00e-02 2.50e+03 ... (remaining 5593 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 89 2.49 - 3.10: 21845 3.10 - 3.70: 43836 3.70 - 4.30: 67025 4.30 - 4.90: 114822 Nonbonded interactions: 247617 Sorted by model distance: nonbonded pdb=" OE2 GLU H 94 " pdb="FE FE H 202 " model vdw 1.892 2.260 nonbonded pdb=" OE1 GLU M 94 " pdb="FE FE M 202 " model vdw 1.953 2.260 nonbonded pdb=" OE2 GLU M 94 " pdb="FE FE M 202 " model vdw 2.025 2.260 nonbonded pdb=" OE1 GLU R 127 " pdb="FE FE R 202 " model vdw 2.054 2.260 nonbonded pdb=" OE2 GLU J 51 " pdb="FE FE J 202 " model vdw 2.056 2.260 ... (remaining 247612 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 156) selection = (chain 'B' and resid 1 through 156) selection = (chain 'C' and resid 1 through 156) selection = (chain 'D' and resid 1 through 156) selection = (chain 'E' and resid 1 through 156) selection = (chain 'F' and resid 1 through 156) selection = (chain 'G' and resid 1 through 156) selection = (chain 'H' and resid 1 through 156) selection = (chain 'I' and resid 1 through 156) selection = (chain 'J' and resid 1 through 156) selection = (chain 'K' and resid 1 through 156) selection = (chain 'L' and resid 1 through 156) selection = (chain 'M' and resid 1 through 156) selection = (chain 'N' and resid 1 through 156) selection = (chain 'O' and resid 1 through 156) selection = (chain 'P' and resid 1 through 156) selection = (chain 'Q' and resid 1 through 156) selection = (chain 'R' and resid 1 through 156) selection = (chain 'S' and resid 1 through 156) selection = (chain 'T' and resid 1 through 156) selection = (chain 'U' and resid 1 through 156) selection = (chain 'V' and resid 1 through 156) selection = (chain 'W' and resid 1 through 156) selection = (chain 'X' and resid 1 through 156) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.890 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: 5.370 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 79.660 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 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 : 0.005 0.090 31968 Z= 0.344 Angle : 0.657 25.824 43354 Z= 0.323 Chirality : 0.036 0.301 4806 Planarity : 0.003 0.063 5596 Dihedral : 15.544 89.366 11862 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % 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: 3.78 (0.13), residues: 3724 helix: 3.44 (0.08), residues: 2994 sheet: None (None), residues: 0 loop : -1.98 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 37 HIS 0.004 0.001 HIS Q 129 PHE 0.048 0.003 PHE V 120 TYR 0.044 0.001 TYR T 71 ARG 0.003 0.000 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.7085 (mtm) cc_final: 0.6558 (mtm) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.4425 time to fit residues: 216.1606 Evaluate side-chains 263 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 3.402 ------------------------------------------------------------------------------- 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: 0.8980 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 282 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 326 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 2 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 31968 Z= 0.196 Angle : 0.533 18.745 43354 Z= 0.238 Chirality : 0.032 0.124 4806 Planarity : 0.003 0.067 5596 Dihedral : 6.959 84.787 4204 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 0.03 % Allowed : 2.38 % Favored : 97.59 % 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: 4.65 (0.13), residues: 3724 helix: 4.18 (0.08), residues: 2948 sheet: None (None), residues: 0 loop : -1.91 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 37 HIS 0.002 0.000 HIS H 130 PHE 0.023 0.002 PHE N 26 TYR 0.022 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 354 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 99 ASP cc_start: 0.8257 (t0) cc_final: 0.8039 (t70) REVERT: I 99 ASP cc_start: 0.8259 (t0) cc_final: 0.8034 (t70) REVERT: L 99 ASP cc_start: 0.8201 (t0) cc_final: 0.7988 (t70) REVERT: M 66 ASP cc_start: 0.7655 (t70) cc_final: 0.7407 (t0) REVERT: N 81 GLN cc_start: 0.8207 (mt0) cc_final: 0.7965 (mt0) REVERT: O 1 MET cc_start: 0.6783 (mtm) cc_final: 0.6410 (mtm) REVERT: O 99 ASP cc_start: 0.8217 (t0) cc_final: 0.8010 (t70) REVERT: V 66 ASP cc_start: 0.7635 (t70) cc_final: 0.7357 (t0) REVERT: W 99 ASP cc_start: 0.8242 (t0) cc_final: 0.8038 (t70) outliers start: 1 outliers final: 0 residues processed: 354 average time/residue: 0.4478 time to fit residues: 249.4293 Evaluate side-chains 340 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 3.472 ------------------------------------------------------------------------------- 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: 10.0000 chunk 101 optimal weight: 9.9990 chunk 272 optimal weight: 7.9990 chunk 222 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 3.9990 chunk 353 optimal weight: 7.9990 chunk 291 optimal weight: 6.9990 chunk 324 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN W 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 31968 Z= 0.411 Angle : 0.688 25.909 43354 Z= 0.306 Chirality : 0.037 0.141 4806 Planarity : 0.004 0.089 5596 Dihedral : 7.017 89.429 4204 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.63 % Allowed : 4.44 % Favored : 94.93 % 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: 3.98 (0.13), residues: 3724 helix: 3.57 (0.08), residues: 3009 sheet: None (None), residues: 0 loop : -2.00 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 37 HIS 0.007 0.001 HIS H 54 PHE 0.026 0.002 PHE R 120 TYR 0.047 0.001 TYR T 71 ARG 0.006 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 267 time to evaluate : 3.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 20 residues processed: 287 average time/residue: 0.4529 time to fit residues: 205.3804 Evaluate side-chains 281 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 261 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 156 optimal weight: 0.0370 chunk 219 optimal weight: 4.9990 chunk 328 optimal weight: 2.9990 chunk 347 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 311 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 overall best weight: 2.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 31968 Z= 0.220 Angle : 0.542 21.197 43354 Z= 0.238 Chirality : 0.032 0.131 4806 Planarity : 0.003 0.058 5596 Dihedral : 6.966 86.358 4204 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.30 % Allowed : 6.04 % Favored : 93.66 % 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: 4.47 (0.13), residues: 3724 helix: 3.98 (0.08), residues: 2985 sheet: None (None), residues: 0 loop : -1.94 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 37 HIS 0.003 0.000 HIS H 54 PHE 0.019 0.001 PHE N 26 TYR 0.043 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 338 time to evaluate : 3.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 ARG cc_start: 0.8711 (mtm-85) cc_final: 0.8469 (mtm180) REVERT: F 50 ASP cc_start: 0.7796 (m-30) cc_final: 0.7513 (m-30) REVERT: M 66 ASP cc_start: 0.7939 (t70) cc_final: 0.7686 (t0) REVERT: N 52 MET cc_start: 0.6325 (OUTLIER) cc_final: 0.6108 (mtt) REVERT: O 1 MET cc_start: 0.6938 (mtm) cc_final: 0.6570 (mtm) REVERT: T 71 TYR cc_start: 0.7899 (m-80) cc_final: 0.7333 (m-80) REVERT: V 66 ASP cc_start: 0.7909 (t70) cc_final: 0.7654 (t0) outliers start: 10 outliers final: 9 residues processed: 345 average time/residue: 0.4404 time to fit residues: 239.1863 Evaluate side-chains 340 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 330 time to evaluate : 3.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 296 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 312 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 31968 Z= 0.308 Angle : 0.596 23.590 43354 Z= 0.264 Chirality : 0.034 0.131 4806 Planarity : 0.003 0.072 5596 Dihedral : 6.919 87.644 4204 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.72 % Allowed : 7.00 % Favored : 92.28 % 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: 4.33 (0.13), residues: 3724 helix: 3.81 (0.08), residues: 2985 sheet: None (None), residues: 0 loop : -1.62 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP O 37 HIS 0.005 0.001 HIS H 54 PHE 0.014 0.002 PHE S 26 TYR 0.038 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 338 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 MET cc_start: 0.6083 (mtt) cc_final: 0.5840 (mtt) REVERT: M 66 ASP cc_start: 0.8052 (t70) cc_final: 0.7767 (t0) REVERT: Q 1 MET cc_start: 0.7480 (ptt) cc_final: 0.7241 (ptt) REVERT: T 71 TYR cc_start: 0.8309 (m-80) cc_final: 0.8094 (m-80) REVERT: V 66 ASP cc_start: 0.8004 (t70) cc_final: 0.7688 (t0) outliers start: 24 outliers final: 23 residues processed: 360 average time/residue: 0.4253 time to fit residues: 246.9662 Evaluate side-chains 337 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 314 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 348 optimal weight: 0.0370 chunk 289 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 31968 Z= 0.232 Angle : 0.546 22.014 43354 Z= 0.244 Chirality : 0.032 0.122 4806 Planarity : 0.003 0.062 5596 Dihedral : 6.874 85.807 4204 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.81 % Allowed : 7.15 % Favored : 92.03 % 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: 4.44 (0.13), residues: 3724 helix: 3.97 (0.08), residues: 2985 sheet: None (None), residues: 0 loop : -2.00 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 37 HIS 0.003 0.000 HIS H 54 PHE 0.016 0.001 PHE N 26 TYR 0.028 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 333 time to evaluate : 3.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 52 MET cc_start: 0.6056 (mtt) cc_final: 0.5851 (mtt) REVERT: M 66 ASP cc_start: 0.7957 (t70) cc_final: 0.7722 (t0) REVERT: O 1 MET cc_start: 0.6935 (mtm) cc_final: 0.6464 (mtm) REVERT: Q 1 MET cc_start: 0.7464 (ptt) cc_final: 0.7237 (ptt) REVERT: V 66 ASP cc_start: 0.7941 (t70) cc_final: 0.7666 (t0) outliers start: 27 outliers final: 26 residues processed: 357 average time/residue: 0.4165 time to fit residues: 239.3136 Evaluate side-chains 348 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 322 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 293 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 346 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 31968 Z= 0.275 Angle : 0.585 24.819 43354 Z= 0.258 Chirality : 0.033 0.147 4806 Planarity : 0.003 0.068 5596 Dihedral : 6.847 87.217 4204 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.97 % Allowed : 7.33 % Favored : 91.70 % 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: 4.43 (0.13), residues: 3724 helix: 3.88 (0.08), residues: 2985 sheet: None (None), residues: 0 loop : -1.59 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 37 HIS 0.004 0.000 HIS H 54 PHE 0.014 0.001 PHE S 26 TYR 0.053 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 327 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 66 ASP cc_start: 0.8014 (t70) cc_final: 0.7744 (t0) REVERT: Q 1 MET cc_start: 0.7482 (ptt) cc_final: 0.7238 (ptt) REVERT: V 66 ASP cc_start: 0.8002 (t70) cc_final: 0.7720 (t0) outliers start: 32 outliers final: 31 residues processed: 357 average time/residue: 0.4209 time to fit residues: 241.8749 Evaluate side-chains 352 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 321 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL 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: 1.9990 chunk 104 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 272 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 31968 Z= 0.226 Angle : 0.558 23.619 43354 Z= 0.242 Chirality : 0.032 0.159 4806 Planarity : 0.003 0.062 5596 Dihedral : 6.852 87.555 4204 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.94 % Allowed : 7.66 % Favored : 91.40 % 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: 4.51 (0.13), residues: 3724 helix: 4.02 (0.08), residues: 2985 sheet: None (None), residues: 0 loop : -2.01 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 37 HIS 0.003 0.000 HIS H 54 PHE 0.016 0.001 PHE N 26 TYR 0.042 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 329 time to evaluate : 3.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 53 ARG cc_start: 0.7420 (mtt90) cc_final: 0.6919 (mtm110) REVERT: O 1 MET cc_start: 0.6929 (mtm) cc_final: 0.6570 (mtm) REVERT: Q 1 MET cc_start: 0.7446 (ptt) cc_final: 0.7208 (ptt) outliers start: 31 outliers final: 30 residues processed: 356 average time/residue: 0.4181 time to fit residues: 239.5630 Evaluate side-chains 352 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 322 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 10.0000 chunk 332 optimal weight: 5.9990 chunk 303 optimal weight: 0.7980 chunk 323 optimal weight: 0.5980 chunk 194 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 292 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 322 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 31968 Z= 0.207 Angle : 0.560 23.933 43354 Z= 0.240 Chirality : 0.032 0.186 4806 Planarity : 0.003 0.057 5596 Dihedral : 6.843 89.176 4204 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.84 % Allowed : 7.97 % Favored : 91.19 % 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: 4.68 (0.13), residues: 3724 helix: 4.20 (0.08), residues: 2967 sheet: None (None), residues: 0 loop : -2.04 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 37 HIS 0.002 0.000 HIS Q 54 PHE 0.018 0.001 PHE R 26 TYR 0.039 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 325 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 53 ARG cc_start: 0.7379 (mtt90) cc_final: 0.6883 (mtm110) REVERT: O 1 MET cc_start: 0.6883 (mtm) cc_final: 0.6569 (mtm) REVERT: Q 1 MET cc_start: 0.7407 (ptt) cc_final: 0.7196 (ptt) REVERT: T 73 ARG cc_start: 0.8626 (mtm180) cc_final: 0.8423 (mtm180) REVERT: V 99 ASP cc_start: 0.8211 (t0) cc_final: 0.8009 (t70) outliers start: 28 outliers final: 28 residues processed: 352 average time/residue: 0.3796 time to fit residues: 213.3928 Evaluate side-chains 353 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 325 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 10.0000 chunk 341 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 237 optimal weight: 0.9980 chunk 358 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 285 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 31968 Z= 0.256 Angle : 0.605 25.615 43354 Z= 0.261 Chirality : 0.033 0.208 4806 Planarity : 0.003 0.063 5596 Dihedral : 6.809 85.575 4204 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.94 % Allowed : 7.91 % Favored : 91.16 % 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: 4.48 (0.13), residues: 3724 helix: 4.01 (0.08), residues: 2985 sheet: None (None), residues: 0 loop : -2.04 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 37 HIS 0.003 0.000 HIS X 54 PHE 0.022 0.001 PHE R 26 TYR 0.046 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 329 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 53 ARG cc_start: 0.7454 (mtt90) cc_final: 0.6983 (mtm110) REVERT: O 1 MET cc_start: 0.6949 (mtm) cc_final: 0.6553 (mtm) REVERT: Q 1 MET cc_start: 0.7425 (ptt) cc_final: 0.7171 (ptt) outliers start: 31 outliers final: 30 residues processed: 357 average time/residue: 0.4388 time to fit residues: 249.6582 Evaluate side-chains 358 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 328 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 8.9990 chunk 304 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 263 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 286 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 293 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.117321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.108308 restraints weight = 28674.112| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 0.57 r_work: 0.2925 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 31968 Z= 0.322 Angle : 0.678 26.909 43354 Z= 0.293 Chirality : 0.034 0.281 4806 Planarity : 0.003 0.077 5596 Dihedral : 6.780 85.691 4204 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.94 % Allowed : 8.03 % Favored : 91.04 % 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: 4.33 (0.13), residues: 3724 helix: 3.81 (0.08), residues: 2985 sheet: None (None), residues: 0 loop : -1.66 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 37 HIS 0.005 0.001 HIS H 54 PHE 0.033 0.002 PHE R 26 TYR 0.059 0.001 TYR T 71 ARG 0.007 0.000 ARG Q 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5505.98 seconds wall clock time: 102 minutes 6.61 seconds (6126.61 seconds total)