Starting phenix.real_space_refine on Thu Mar 21 23:29:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6f_33639/03_2024/7y6f_33639_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6f_33639/03_2024/7y6f_33639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6f_33639/03_2024/7y6f_33639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6f_33639/03_2024/7y6f_33639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6f_33639/03_2024/7y6f_33639_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6f_33639/03_2024/7y6f_33639_trim_updated.pdb" } resolution = 2.7 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= 0.014 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 59 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 4": "OD1" <-> "OD2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "B ASP 4": "OD1" <-> "OD2" Residue "B TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 33": "OD1" <-> "OD2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "E GLU 9": "OE1" <-> "OE2" Residue "E TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "F ASP 4": "OD1" <-> "OD2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 33": "OD1" <-> "OD2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F ASP 99": "OD1" <-> "OD2" Residue "F ASP 126": "OD1" <-> "OD2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F ASP 132": "OD1" <-> "OD2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "G GLU 9": "OE1" <-> "OE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "G TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G ASP 132": "OD1" <-> "OD2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "H GLU 9": "OE1" <-> "OE2" Residue "H TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H GLU 135": "OE1" <-> "OE2" Residue "H ASP 139": "OD1" <-> "OD2" Residue "I ASP 4": "OD1" <-> "OD2" Residue "I TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I ASP 139": "OD1" <-> "OD2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "J ASP 4": "OD1" <-> "OD2" Residue "J TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 33": "OD1" <-> "OD2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 50": "OD1" <-> "OD2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J ASP 126": "OD1" <-> "OD2" Residue "J ASP 132": "OD1" <-> "OD2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "K ASP 4": "OD1" <-> "OD2" Residue "K TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 50": "OD1" <-> "OD2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 127": "OE1" <-> "OE2" Residue "K GLU 128": "OE1" <-> "OE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "L PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 56": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L ASP 126": "OD1" <-> "OD2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "L GLU 135": "OE1" <-> "OE2" Residue "L GLU 146": "OE1" <-> "OE2" Residue "M ASP 33": "OD1" <-> "OD2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M ASP 132": "OD1" <-> "OD2" Residue "N TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N ASP 99": "OD1" <-> "OD2" Residue "N ASP 126": "OD1" <-> "OD2" Residue "N GLU 127": "OE1" <-> "OE2" Residue "N GLU 135": "OE1" <-> "OE2" Residue "N ASP 139": "OD1" <-> "OD2" Residue "O PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 33": "OD1" <-> "OD2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O GLU 92": "OE1" <-> "OE2" Residue "O GLU 96": "OE1" <-> "OE2" Residue "O ASP 99": "OD1" <-> "OD2" Residue "O ASP 126": "OD1" <-> "OD2" Residue "O GLU 127": "OE1" <-> "OE2" Residue "O ASP 132": "OD1" <-> "OD2" Residue "O GLU 135": "OE1" <-> "OE2" Residue "O GLU 142": "OE1" <-> "OE2" Residue "O GLU 146": "OE1" <-> "OE2" Residue "P ASP 4": "OD1" <-> "OD2" Residue "P TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "P ASP 50": "OD1" <-> "OD2" Residue "P GLU 51": "OE1" <-> "OE2" Residue "P ASP 126": "OD1" <-> "OD2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P ASP 132": "OD1" <-> "OD2" Residue "P GLU 135": "OE1" <-> "OE2" Residue "P ASP 139": "OD1" <-> "OD2" Residue "Q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 47": "OE1" <-> "OE2" Residue "Q ASP 50": "OD1" <-> "OD2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "Q ASP 126": "OD1" <-> "OD2" Residue "Q GLU 127": "OE1" <-> "OE2" Residue "Q ASP 132": "OD1" <-> "OD2" Residue "Q GLU 135": "OE1" <-> "OE2" Residue "R ASP 4": "OD1" <-> "OD2" Residue "R GLU 9": "OE1" <-> "OE2" Residue "R GLU 18": "OE1" <-> "OE2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 47": "OE1" <-> "OE2" Residue "R ASP 50": "OD1" <-> "OD2" Residue "R GLU 92": "OE1" <-> "OE2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R ASP 99": "OD1" <-> "OD2" Residue "R GLU 135": "OE1" <-> "OE2" Residue "R ASP 139": "OD1" <-> "OD2" Residue "S TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "S ASP 50": "OD1" <-> "OD2" Residue "S GLU 92": "OE1" <-> "OE2" Residue "S ASP 99": "OD1" <-> "OD2" Residue "S GLU 121": "OE1" <-> "OE2" Residue "S GLU 127": "OE1" <-> "OE2" Residue "S GLU 135": "OE1" <-> "OE2" Residue "S GLU 146": "OE1" <-> "OE2" Residue "T GLU 9": "OE1" <-> "OE2" Residue "T TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 50": "OD1" <-> "OD2" Residue "T GLU 92": "OE1" <-> "OE2" Residue "T GLU 127": "OE1" <-> "OE2" Residue "T ASP 132": "OD1" <-> "OD2" Residue "T GLU 135": "OE1" <-> "OE2" Residue "U ASP 4": "OD1" <-> "OD2" Residue "U TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 50": "OD1" <-> "OD2" Residue "U GLU 51": "OE1" <-> "OE2" Residue "U GLU 92": "OE1" <-> "OE2" Residue "U GLU 121": "OE1" <-> "OE2" Residue "U ASP 126": "OD1" <-> "OD2" Residue "U GLU 127": "OE1" <-> "OE2" Residue "U GLU 128": "OE1" <-> "OE2" Residue "U GLU 135": "OE1" <-> "OE2" Residue "U ASP 139": "OD1" <-> "OD2" Residue "V GLU 18": "OE1" <-> "OE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ASP 50": "OD1" <-> "OD2" Residue "V GLU 51": "OE1" <-> "OE2" Residue "V GLU 92": "OE1" <-> "OE2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "V TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 4": "OD1" <-> "OD2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 50": "OD1" <-> "OD2" Residue "W GLU 85": "OE1" <-> "OE2" Residue "W ASP 99": "OD1" <-> "OD2" Residue "W GLU 127": "OE1" <-> "OE2" Residue "W GLU 135": "OE1" <-> "OE2" Residue "W GLU 146": "OE1" <-> "OE2" Residue "X ASP 4": "OD1" <-> "OD2" Residue "X GLU 18": "OE1" <-> "OE2" Residue "X TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 47": "OE1" <-> "OE2" Residue "X ASP 50": "OD1" <-> "OD2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X GLU 85": "OE1" <-> "OE2" Residue "X GLU 92": "OE1" <-> "OE2" Residue "X ASP 99": "OD1" <-> "OD2" Residue "X GLU 127": "OE1" <-> "OE2" Residue "X GLU 135": "OE1" <-> "OE2" Residue "X ASP 139": "OD1" <-> "OD2" 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: 31427 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: 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: "K" 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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 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: 16.10, per 1000 atoms: 0.51 Number of scatterers: 31427 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 59 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.86 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 80.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 Processing helix chain 'A' and resid 38 through 65 removed outlier: 3.520A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 111 removed outlier: 3.656A 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: 4.132A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 35 Processing helix chain 'B' and resid 38 through 65 removed outlier: 3.614A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 111 removed outlier: 3.666A 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: 3.944A 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: 3.500A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 111 removed outlier: 3.654A 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: 4.096A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 35 Processing helix chain 'D' and resid 38 through 65 removed outlier: 3.568A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 111 removed outlier: 3.624A pdb=" N LYS D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 144 Processing helix chain 'D' and resid 146 through 152 removed outlier: 4.014A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 Processing helix chain 'E' and resid 38 through 65 removed outlier: 3.515A pdb=" N LEU E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 111 removed outlier: 3.662A 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: 4.095A pdb=" N THR E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 35 Processing helix chain 'F' and resid 38 through 65 removed outlier: 3.520A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 111 removed outlier: 3.671A 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: 4.066A 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: 3.649A 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: 4.094A pdb=" N THR G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 35 Processing helix chain 'H' and resid 38 through 65 removed outlier: 3.508A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 111 removed outlier: 3.664A 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: 3.976A pdb=" N THR H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 35 Processing helix chain 'I' and resid 38 through 65 removed outlier: 3.520A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 111 removed outlier: 3.638A 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: 3.929A 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: 3.520A pdb=" N LEU J 65 " --> pdb=" O ARG J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 111 removed outlier: 3.628A 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: 4.129A pdb=" N THR J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 35 Processing helix chain 'K' and resid 38 through 65 removed outlier: 3.616A 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: 3.663A 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: 3.957A pdb=" N THR K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 35 removed outlier: 3.510A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 65 removed outlier: 3.626A pdb=" N ALA L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 111 Processing helix chain 'L' and resid 114 through 144 Processing helix chain 'L' and resid 146 through 152 removed outlier: 4.159A 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: 3.506A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 144 removed outlier: 3.700A pdb=" N ASP M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 152 removed outlier: 3.997A pdb=" N THR M 152 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 35 Processing helix chain 'N' and resid 38 through 65 Processing helix chain 'N' and resid 83 through 111 removed outlier: 3.677A 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: 4.087A 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: 3.539A 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: 3.940A 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: 3.611A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 111 removed outlier: 3.656A 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: 3.890A 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 Processing helix chain 'Q' and resid 83 through 111 removed outlier: 3.629A 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: 4.089A 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: 3.572A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 111 removed outlier: 3.649A 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: 4.046A pdb=" N THR R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 35 Processing helix chain 'S' and resid 38 through 65 removed outlier: 3.519A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 111 removed outlier: 3.674A 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: 4.074A pdb=" N THR S 152 " --> pdb=" O LEU S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 35 Processing helix chain 'T' and resid 38 through 65 removed outlier: 3.520A pdb=" N LEU T 65 " --> pdb=" O ARG T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 111 removed outlier: 3.654A 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: 4.025A pdb=" N THR T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 35 removed outlier: 3.542A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 65 removed outlier: 3.608A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 111 removed outlier: 3.657A 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: 4.033A 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 Processing helix chain 'V' and resid 114 through 144 removed outlier: 3.699A pdb=" N ASP V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 152 removed outlier: 4.152A 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: 3.969A pdb=" N LYS W 42 " --> pdb=" O THR W 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 111 removed outlier: 3.652A 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: 4.063A pdb=" N THR W 152 " --> pdb=" O LEU W 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 35 Processing helix chain 'X' and resid 38 through 65 removed outlier: 3.570A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 111 removed outlier: 3.682A 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: 4.076A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 2466 hydrogen bonds defined for protein. 7398 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: 9.06 Time building geometry restraints manager: 13.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.41: 13351 1.41 - 1.59: 18377 1.59 - 1.78: 6 1.78 - 1.96: 186 1.96 - 2.14: 48 Bond restraints: 31968 Sorted by residual: bond pdb=" C GLN W 14 " pdb=" N LEU W 15 " ideal model delta sigma weight residual 1.335 1.407 -0.072 1.31e-02 5.83e+03 3.01e+01 bond pdb=" C GLU W 13 " pdb=" N GLN W 14 " ideal model delta sigma weight residual 1.335 1.405 -0.070 1.31e-02 5.83e+03 2.89e+01 bond pdb=" CB MET Q 52 " pdb=" CG MET Q 52 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CGA HEM C 203 " pdb=" O2A HEM C 203 " ideal model delta sigma weight residual 1.258 1.288 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" NB HEM S 203 " pdb="FE HEM S 203 " ideal model delta sigma weight residual 2.080 1.975 0.105 7.00e-02 2.04e+02 2.25e+00 ... (remaining 31963 not shown) Histogram of bond angle deviations from ideal: 83.42 - 102.60: 148 102.60 - 121.79: 36583 121.79 - 140.97: 6599 140.97 - 160.15: 2 160.15 - 179.33: 22 Bond angle restraints: 43354 Sorted by residual: angle pdb=" CB MET C 52 " pdb=" CG MET C 52 " pdb=" SD MET C 52 " ideal model delta sigma weight residual 112.70 83.42 29.28 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CB MET X 52 " pdb=" CG MET X 52 " pdb=" SD MET X 52 " ideal model delta sigma weight residual 112.70 93.08 19.62 3.00e+00 1.11e-01 4.28e+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 93.25 19.45 3.00e+00 1.11e-01 4.20e+01 angle pdb=" O GLN W 14 " pdb=" C GLN W 14 " pdb=" N LEU W 15 " ideal model delta sigma weight residual 122.12 115.48 6.64 1.06e+00 8.90e-01 3.92e+01 angle pdb=" CB MET N 52 " pdb=" CG MET N 52 " pdb=" SD MET N 52 " ideal model delta sigma weight residual 112.70 95.16 17.54 3.00e+00 1.11e-01 3.42e+01 ... (remaining 43349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 16867 17.68 - 35.35: 1827 35.35 - 53.03: 296 53.03 - 70.70: 99 70.70 - 88.38: 29 Dihedral angle restraints: 19118 sinusoidal: 7994 harmonic: 11124 Sorted by residual: dihedral pdb=" C2B HEM S 203 " pdb=" C3B HEM S 203 " pdb=" CAB HEM S 203 " pdb=" CBB HEM S 203 " ideal model delta sinusoidal sigma weight residual 0.00 32.74 -32.74 2 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CA GLU Q 51 " pdb=" C GLU Q 51 " pdb=" N MET Q 52 " pdb=" CA MET Q 52 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" C2B HEM K 203 " pdb=" C3B HEM K 203 " pdb=" CAB HEM K 203 " pdb=" CBB HEM K 203 " ideal model delta sinusoidal sigma weight residual 0.00 -30.74 30.74 2 1.00e+01 1.00e-02 1.25e+01 ... (remaining 19115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3785 0.034 - 0.069: 722 0.069 - 0.103: 269 0.103 - 0.137: 28 0.137 - 0.172: 2 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 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA PHE F 49 " pdb=" N PHE F 49 " pdb=" C PHE F 49 " pdb=" CB PHE F 49 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA MET C 52 " pdb=" N MET C 52 " pdb=" C MET C 52 " pdb=" CB MET C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 4803 not shown) Planarity restraints: 5596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 45 " -0.450 9.50e-02 1.11e+02 2.02e-01 2.63e+01 pdb=" NE ARG R 45 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG R 45 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG R 45 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG R 45 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 49 " 0.016 2.00e-02 2.50e+03 2.93e-02 1.50e+01 pdb=" CG PHE F 49 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE F 49 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE F 49 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE F 49 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE F 49 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 49 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM C 203 " 0.011 2.00e-02 2.50e+03 2.11e-02 1.00e+01 pdb=" C2A HEM C 203 " 0.028 2.00e-02 2.50e+03 pdb=" C3A HEM C 203 " 0.010 2.00e-02 2.50e+03 pdb=" C4A HEM C 203 " 0.004 2.00e-02 2.50e+03 pdb=" CAA HEM C 203 " -0.032 2.00e-02 2.50e+03 pdb=" CHA HEM C 203 " 0.017 2.00e-02 2.50e+03 pdb=" CHB HEM C 203 " 0.003 2.00e-02 2.50e+03 pdb=" CMA HEM C 203 " 0.001 2.00e-02 2.50e+03 pdb=" NA HEM C 203 " -0.041 2.00e-02 2.50e+03 ... (remaining 5593 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 74 2.43 - 3.04: 19765 3.04 - 3.66: 43966 3.66 - 4.28: 68656 4.28 - 4.90: 116050 Nonbonded interactions: 248511 Sorted by model distance: nonbonded pdb=" OE2 GLU H 94 " pdb="FE FE H 202 " model vdw 1.807 2.260 nonbonded pdb=" OE1 GLU G 127 " pdb="FE FE G 202 " model vdw 1.953 2.260 nonbonded pdb=" OE1 GLU T 127 " pdb="FE FE2 T 203 " model vdw 1.972 3.000 nonbonded pdb=" OE1 GLU F 127 " pdb="FE FE2 F 202 " model vdw 1.974 3.000 nonbonded pdb=" OE1 GLU R 127 " pdb="FE FE R 202 " model vdw 2.031 2.260 ... (remaining 248506 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: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.020 Extract box with map and model: 5.380 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 79.090 Find NCS groups from input model: 2.550 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: 0.000 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 31968 Z= 0.210 Angle : 0.618 31.860 43354 Z= 0.323 Chirality : 0.033 0.172 4806 Planarity : 0.004 0.202 5596 Dihedral : 15.053 88.377 11862 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 4.11 (0.13), residues: 3724 helix: 3.83 (0.08), residues: 2999 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 37 HIS 0.003 0.001 HIS U 54 PHE 0.062 0.003 PHE F 49 TYR 0.047 0.001 TYR T 71 ARG 0.019 0.000 ARG R 45 *********************** 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 712 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 712 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.5264 (mtm) cc_final: 0.5011 (mtm) REVERT: L 129 HIS cc_start: 0.7173 (m-70) cc_final: 0.6954 (m90) REVERT: S 146 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8137 (mm-30) outliers start: 0 outliers final: 0 residues processed: 712 average time/residue: 1.4196 time to fit residues: 1184.4551 Evaluate side-chains 655 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 655 time to evaluate : 3.689 ------------------------------------------------------------------------------- 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: 2.9990 chunk 272 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 282 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 HIS ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 137 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN T 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 31968 Z= 0.255 Angle : 0.592 13.301 43354 Z= 0.287 Chirality : 0.034 0.163 4806 Planarity : 0.004 0.085 5596 Dihedral : 6.952 81.974 4204 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.05 % Allowed : 7.00 % Favored : 90.95 % 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: 4.31 (0.13), residues: 3724 helix: 3.80 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.01 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 37 HIS 0.005 0.001 HIS Q 129 PHE 0.037 0.003 PHE F 49 TYR 0.046 0.002 TYR T 71 ARG 0.004 0.000 ARG S 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 773 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 705 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8220 (mt) REVERT: K 68 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8233 (mt) REVERT: L 66 ASP cc_start: 0.7615 (t70) cc_final: 0.7375 (t0) REVERT: L 129 HIS cc_start: 0.7306 (m-70) cc_final: 0.7074 (m90) REVERT: N 66 ASP cc_start: 0.7772 (t0) cc_final: 0.7533 (t0) REVERT: P 9 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: Q 66 ASP cc_start: 0.7848 (t0) cc_final: 0.7601 (t0) REVERT: S 66 ASP cc_start: 0.7827 (t0) cc_final: 0.7584 (t0) REVERT: U 68 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8231 (mt) REVERT: W 66 ASP cc_start: 0.7870 (t0) cc_final: 0.7611 (t0) REVERT: X 66 ASP cc_start: 0.7870 (t0) cc_final: 0.7610 (t0) REVERT: X 68 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8192 (mt) outliers start: 68 outliers final: 7 residues processed: 714 average time/residue: 1.4843 time to fit residues: 1235.1989 Evaluate side-chains 711 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 699 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 68 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 272 optimal weight: 0.9980 chunk 222 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 5.9990 chunk 353 optimal weight: 0.7980 chunk 291 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1203 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= 0.237 Angle : 0.603 23.999 43354 Z= 0.277 Chirality : 0.033 0.332 4806 Planarity : 0.003 0.067 5596 Dihedral : 7.129 86.965 4204 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.11 % Allowed : 8.54 % Favored : 89.35 % 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: 3.96 (0.08), residues: 3005 sheet: None (None), residues: 0 loop : -2.16 (0.22), residues: 719 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 0.027 0.002 PHE O 120 TYR 0.035 0.001 TYR T 71 ARG 0.003 0.000 ARG S 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 754 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 684 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8305 (mt) REVERT: B 68 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8282 (mt) REVERT: C 68 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8267 (mt) REVERT: E 68 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8205 (mt) REVERT: E 81 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7447 (mt0) REVERT: F 68 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8247 (mt) REVERT: G 68 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8340 (mt) REVERT: G 81 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7429 (mt0) REVERT: H 68 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8322 (mt) REVERT: I 68 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8324 (mt) REVERT: J 68 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8232 (mt) REVERT: L 66 ASP cc_start: 0.7640 (t70) cc_final: 0.7437 (t0) REVERT: L 68 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8318 (mt) REVERT: L 81 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: L 129 HIS cc_start: 0.7292 (m-70) cc_final: 0.7074 (m90) REVERT: M 1 MET cc_start: 0.6004 (mmp) cc_final: 0.5538 (mmm) REVERT: N 68 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8270 (mt) REVERT: O 68 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8350 (mt) REVERT: P 68 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8311 (mt) REVERT: Q 66 ASP cc_start: 0.7817 (t0) cc_final: 0.7559 (t0) REVERT: Q 68 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8276 (mt) REVERT: Q 81 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: R 68 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8305 (mt) REVERT: S 66 ASP cc_start: 0.7782 (t0) cc_final: 0.7514 (t0) REVERT: S 68 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8257 (mt) REVERT: U 81 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7445 (mt0) REVERT: W 66 ASP cc_start: 0.7843 (t0) cc_final: 0.7553 (t0) REVERT: W 68 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8256 (mt) REVERT: X 66 ASP cc_start: 0.7807 (t0) cc_final: 0.7508 (t0) outliers start: 70 outliers final: 10 residues processed: 694 average time/residue: 1.5031 time to fit residues: 1214.9495 Evaluate side-chains 702 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 670 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 35 LYS Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain Q residue 35 LYS Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 68 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 4.9990 chunk 246 optimal weight: 0.0770 chunk 169 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 328 optimal weight: 0.9980 chunk 347 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 156 GLN J 112 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1280 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= 0.192 Angle : 0.511 20.170 43354 Z= 0.238 Chirality : 0.032 0.257 4806 Planarity : 0.003 0.053 5596 Dihedral : 7.087 88.219 4204 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.56 % Allowed : 9.32 % Favored : 88.11 % 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: 4.69 (0.13), residues: 3724 helix: 4.23 (0.08), residues: 3005 sheet: None (None), residues: 0 loop : -2.56 (0.19), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 37 HIS 0.003 0.000 HIS Q 129 PHE 0.016 0.001 PHE F 49 TYR 0.022 0.001 TYR T 71 ARG 0.002 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 764 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 679 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8271 (mt) REVERT: B 68 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8263 (mt) REVERT: F 68 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8197 (mt) REVERT: G 68 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8294 (mt) REVERT: I 68 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8272 (mt) REVERT: J 68 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8145 (mt) REVERT: M 1 MET cc_start: 0.5957 (mmp) cc_final: 0.5544 (mmm) REVERT: P 68 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8272 (mt) REVERT: R 68 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8258 (mt) REVERT: T 86 MET cc_start: 0.6672 (mtt) cc_final: 0.6459 (mtt) REVERT: V 1 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6696 (ttm) outliers start: 85 outliers final: 16 residues processed: 691 average time/residue: 1.4536 time to fit residues: 1173.9789 Evaluate side-chains 674 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 649 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain U residue 60 ASP Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain V residue 60 ASP Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain X residue 60 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 240 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 31968 Z= 0.300 Angle : 0.650 28.094 43354 Z= 0.309 Chirality : 0.036 0.123 4806 Planarity : 0.004 0.063 5596 Dihedral : 7.370 86.312 4204 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.23 % Allowed : 11.26 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.28 (0.13), residues: 3724 helix: 3.72 (0.08), residues: 3042 sheet: None (None), residues: 0 loop : -1.88 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP P 37 HIS 0.005 0.001 HIS Q 129 PHE 0.019 0.002 PHE F 49 TYR 0.039 0.002 TYR T 71 ARG 0.004 0.001 ARG S 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 826 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 752 time to evaluate : 3.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8320 (mt) REVERT: B 68 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8302 (mt) REVERT: D 81 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: F 68 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8306 (mt) REVERT: G 68 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8347 (mt) REVERT: G 81 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7429 (mt0) REVERT: I 68 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8315 (mt) REVERT: J 68 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8289 (mt) REVERT: J 81 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: K 9 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: K 81 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7446 (mt0) REVERT: L 66 ASP cc_start: 0.7834 (t70) cc_final: 0.7586 (t0) REVERT: L 81 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: M 1 MET cc_start: 0.6278 (mmp) cc_final: 0.5801 (mmm) REVERT: M 66 ASP cc_start: 0.7871 (t70) cc_final: 0.7556 (t0) REVERT: N 81 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: O 68 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8344 (mt) REVERT: P 68 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8327 (mt) REVERT: R 68 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8313 (mt) REVERT: R 81 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7128 (mt0) REVERT: S 66 ASP cc_start: 0.7893 (t0) cc_final: 0.7572 (t0) REVERT: V 1 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6726 (ttm) REVERT: W 81 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7295 (mt0) outliers start: 74 outliers final: 6 residues processed: 763 average time/residue: 1.5369 time to fit residues: 1360.6285 Evaluate side-chains 773 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 748 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 81 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 5.9990 chunk 313 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 348 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 31968 Z= 0.261 Angle : 0.618 21.258 43354 Z= 0.288 Chirality : 0.034 0.119 4806 Planarity : 0.003 0.051 5596 Dihedral : 7.458 85.676 4204 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.72 % Allowed : 12.25 % Favored : 86.03 % 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: 4.29 (0.13), residues: 3724 helix: 3.79 (0.08), residues: 3023 sheet: None (None), residues: 0 loop : -2.01 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 37 HIS 0.004 0.001 HIS Q 129 PHE 0.027 0.002 PHE F 49 TYR 0.030 0.002 TYR T 71 ARG 0.003 0.000 ARG S 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 767 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 710 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3923 (OUTLIER) cc_final: 0.3567 (mmm) REVERT: A 68 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8313 (mt) REVERT: B 68 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8289 (mt) REVERT: D 81 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: E 1 MET cc_start: 0.3906 (OUTLIER) cc_final: 0.3526 (mmm) REVERT: E 81 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7458 (mt0) REVERT: F 68 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8308 (mt) REVERT: G 68 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8329 (mt) REVERT: G 81 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: I 68 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8302 (mt) REVERT: J 68 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8276 (mt) REVERT: J 81 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: K 68 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8288 (mt) REVERT: K 81 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: L 66 ASP cc_start: 0.7746 (t70) cc_final: 0.7520 (t0) REVERT: L 68 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8326 (mt) REVERT: L 81 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7359 (mt0) REVERT: M 1 MET cc_start: 0.6161 (mmp) cc_final: 0.5877 (mmm) REVERT: N 68 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8271 (mt) REVERT: N 81 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7673 (mt0) REVERT: O 68 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8339 (mt) REVERT: P 68 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8326 (mt) REVERT: R 68 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8289 (mt) REVERT: S 66 ASP cc_start: 0.7883 (t0) cc_final: 0.7547 (t0) REVERT: S 68 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8268 (mt) REVERT: T 68 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8281 (mt) REVERT: V 1 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6680 (ttm) REVERT: V 68 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8258 (mt) REVERT: W 66 ASP cc_start: 0.7915 (t0) cc_final: 0.7583 (t0) REVERT: W 68 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8280 (mt) REVERT: X 68 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8314 (mt) outliers start: 57 outliers final: 15 residues processed: 718 average time/residue: 1.5318 time to fit residues: 1286.5082 Evaluate side-chains 748 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 706 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 13 GLU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 35 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain X residue 68 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 346 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 31968 Z= 0.279 Angle : 0.633 22.902 43354 Z= 0.297 Chirality : 0.035 0.165 4806 Planarity : 0.003 0.061 5596 Dihedral : 7.497 89.463 4204 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.66 % Allowed : 12.61 % Favored : 84.73 % 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: 4.19 (0.13), residues: 3724 helix: 3.72 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.03 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 37 HIS 0.005 0.001 HIS H 54 PHE 0.022 0.002 PHE F 49 TYR 0.027 0.002 TYR T 71 ARG 0.004 0.000 ARG G 73 *********************** 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 819 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 731 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3976 (OUTLIER) cc_final: 0.3770 (mmm) REVERT: A 68 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8329 (mt) REVERT: B 68 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8297 (mt) REVERT: C 81 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7476 (mt0) REVERT: D 68 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8340 (mt) REVERT: D 81 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7648 (mt0) REVERT: E 1 MET cc_start: 0.4002 (OUTLIER) cc_final: 0.3701 (mmm) REVERT: E 81 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7485 (mt0) REVERT: F 68 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8332 (mt) REVERT: G 68 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8333 (mt) REVERT: G 81 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7396 (mt0) REVERT: H 68 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8322 (mt) REVERT: I 68 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8307 (mt) REVERT: J 68 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8294 (mt) REVERT: J 81 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: K 81 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7436 (mt0) REVERT: L 66 ASP cc_start: 0.7807 (t70) cc_final: 0.7552 (t0) REVERT: L 68 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8337 (mt) REVERT: L 81 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: M 66 ASP cc_start: 0.7819 (t70) cc_final: 0.7531 (t0) REVERT: N 68 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8295 (mt) REVERT: N 81 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7643 (mt0) REVERT: O 68 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8346 (mt) REVERT: P 68 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8321 (mt) REVERT: R 68 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8284 (mt) REVERT: R 81 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7151 (mt0) REVERT: S 66 ASP cc_start: 0.7877 (t0) cc_final: 0.7548 (t0) REVERT: S 68 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8276 (mt) REVERT: T 68 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8292 (mt) REVERT: V 1 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6660 (ttm) REVERT: V 68 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8316 (mt) REVERT: W 66 ASP cc_start: 0.7951 (t0) cc_final: 0.7607 (t0) REVERT: W 68 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8320 (mt) REVERT: X 1 MET cc_start: 0.3767 (OUTLIER) cc_final: 0.3561 (mmm) REVERT: X 68 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8344 (mt) outliers start: 88 outliers final: 19 residues processed: 743 average time/residue: 1.4790 time to fit residues: 1280.8576 Evaluate side-chains 775 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 725 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 13 GLU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 35 LYS Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 68 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 31968 Z= 0.287 Angle : 0.729 36.143 43354 Z= 0.319 Chirality : 0.035 0.213 4806 Planarity : 0.003 0.060 5596 Dihedral : 7.576 89.335 4204 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.08 % Allowed : 13.88 % Favored : 84.04 % 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: 4.13 (0.13), residues: 3724 helix: 3.67 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.04 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 37 HIS 0.005 0.001 HIS H 54 PHE 0.030 0.002 PHE F 49 TYR 0.026 0.002 TYR T 71 ARG 0.005 0.001 ARG G 73 *********************** 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 806 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 737 time to evaluate : 3.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3943 (OUTLIER) cc_final: 0.3634 (mmm) REVERT: A 68 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8330 (mt) REVERT: B 68 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8312 (mt) REVERT: C 68 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8283 (mt) REVERT: C 81 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: D 68 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8366 (mt) REVERT: D 81 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: E 1 MET cc_start: 0.4000 (OUTLIER) cc_final: 0.3664 (mmm) REVERT: E 81 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7448 (mt0) REVERT: F 68 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8329 (mt) REVERT: G 68 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8330 (mt) REVERT: G 81 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7426 (mt0) REVERT: H 68 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8353 (mt) REVERT: I 68 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8306 (mt) REVERT: I 81 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: J 68 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8290 (mt) REVERT: J 81 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: K 81 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7469 (mt0) REVERT: L 66 ASP cc_start: 0.7819 (t70) cc_final: 0.7553 (t0) REVERT: L 68 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8332 (mt) REVERT: L 81 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7368 (mt0) REVERT: M 66 ASP cc_start: 0.7847 (t70) cc_final: 0.7579 (t0) REVERT: N 68 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8285 (mt) REVERT: N 81 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7666 (mt0) REVERT: O 68 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8339 (mt) REVERT: P 68 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8323 (mt) REVERT: R 68 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8305 (mt) REVERT: R 81 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7126 (mt0) REVERT: S 66 ASP cc_start: 0.7895 (t0) cc_final: 0.7569 (t0) REVERT: S 68 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8305 (mt) REVERT: S 81 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7052 (mt0) REVERT: T 81 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7066 (mt0) REVERT: U 68 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8329 (mt) REVERT: U 81 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: V 1 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6632 (ttm) REVERT: W 66 ASP cc_start: 0.7949 (t0) cc_final: 0.7603 (t0) REVERT: W 68 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8325 (mt) REVERT: X 1 MET cc_start: 0.3756 (OUTLIER) cc_final: 0.3519 (mmm) REVERT: X 68 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8332 (mt) outliers start: 69 outliers final: 19 residues processed: 750 average time/residue: 1.4979 time to fit residues: 1306.9381 Evaluate side-chains 786 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 732 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 13 GLU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 35 LYS Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 81 GLN Chi-restraints excluded: chain T residue 81 GLN Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 68 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 5.9990 chunk 332 optimal weight: 9.9990 chunk 303 optimal weight: 3.9990 chunk 323 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 292 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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: 0.8241 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 31968 Z= 0.254 Angle : 0.676 38.659 43354 Z= 0.293 Chirality : 0.034 0.293 4806 Planarity : 0.003 0.059 5596 Dihedral : 7.445 87.156 4204 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.96 % Allowed : 14.33 % Favored : 83.71 % 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: 4.34 (0.13), residues: 3724 helix: 3.87 (0.08), residues: 3005 sheet: None (None), residues: 0 loop : -2.03 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 37 HIS 0.004 0.001 HIS H 54 PHE 0.029 0.001 PHE F 49 TYR 0.021 0.001 TYR T 71 ARG 0.004 0.000 ARG G 73 *********************** 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 750 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 685 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3827 (OUTLIER) cc_final: 0.3610 (mmm) REVERT: A 68 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8321 (mt) REVERT: B 68 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8291 (mt) REVERT: C 81 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: D 68 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8312 (mt) REVERT: D 81 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: E 1 MET cc_start: 0.3767 (OUTLIER) cc_final: 0.3542 (mmm) REVERT: E 81 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: F 68 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8322 (mt) REVERT: G 68 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8337 (mt) REVERT: G 81 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7334 (mt0) REVERT: H 68 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8321 (mt) REVERT: I 68 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8311 (mt) REVERT: I 81 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: J 81 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: K 81 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: L 66 ASP cc_start: 0.7703 (t70) cc_final: 0.7482 (t0) REVERT: L 81 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7362 (mt0) REVERT: N 81 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7621 (mt0) REVERT: P 1 MET cc_start: 0.3951 (OUTLIER) cc_final: 0.3643 (mmm) REVERT: P 68 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8322 (mt) REVERT: R 68 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8281 (mt) REVERT: R 81 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7101 (mt0) REVERT: S 66 ASP cc_start: 0.7811 (t0) cc_final: 0.7522 (t0) REVERT: T 81 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7091 (mt0) REVERT: U 81 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7442 (mt0) REVERT: V 1 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6669 (ttm) REVERT: V 68 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8220 (mt) REVERT: W 66 ASP cc_start: 0.7840 (t0) cc_final: 0.7532 (t0) outliers start: 65 outliers final: 24 residues processed: 697 average time/residue: 1.4552 time to fit residues: 1184.9445 Evaluate side-chains 732 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 682 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 13 GLU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 35 LYS Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 13 GLU Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain T residue 81 GLN Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 13 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 20.0000 chunk 341 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 358 optimal weight: 0.9990 chunk 330 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.197 31968 Z= 0.322 Angle : 0.824 44.461 43354 Z= 0.350 Chirality : 0.037 0.294 4806 Planarity : 0.004 0.067 5596 Dihedral : 7.376 86.275 4204 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.72 % Allowed : 14.21 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3.93 (0.13), residues: 3724 helix: 3.48 (0.08), residues: 3042 sheet: None (None), residues: 0 loop : -1.98 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP S 37 HIS 0.007 0.001 HIS H 54 PHE 0.038 0.002 PHE F 49 TYR 0.030 0.002 TYR T 71 ARG 0.007 0.001 ARG J 73 ********************** 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 849 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 759 time to evaluate : 3.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8325 (mt) REVERT: B 68 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8345 (mt) REVERT: C 81 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: D 81 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: E 81 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7494 (mt0) REVERT: F 68 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8365 (mt) REVERT: G 68 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8368 (mt) REVERT: G 81 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: I 68 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8344 (mt) REVERT: I 81 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7487 (mt0) REVERT: J 81 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: K 81 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7456 (mt0) REVERT: L 66 ASP cc_start: 0.7861 (t70) cc_final: 0.7548 (t0) REVERT: L 81 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7382 (mt0) REVERT: M 66 ASP cc_start: 0.7884 (t70) cc_final: 0.7573 (t0) REVERT: N 81 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: O 66 ASP cc_start: 0.7813 (t70) cc_final: 0.7458 (t0) REVERT: P 68 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8356 (mt) REVERT: Q 81 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7475 (mt0) REVERT: R 68 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8371 (mt) REVERT: R 81 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7087 (mt0) REVERT: T 81 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7183 (mt0) REVERT: U 81 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: V 1 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6682 (ttm) outliers start: 90 outliers final: 30 residues processed: 777 average time/residue: 1.5332 time to fit residues: 1380.5121 Evaluate side-chains 801 residues out of total 3340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 750 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 13 GLU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 35 LYS Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 13 GLU Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain T residue 81 GLN Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 13 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 263 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 286 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 293 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.163001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.157448 restraints weight = 25804.616| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 0.31 r_work: 0.3534 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 31968 Z= 0.194 Angle : 0.670 37.060 43354 Z= 0.278 Chirality : 0.032 0.180 4806 Planarity : 0.003 0.050 5596 Dihedral : 7.251 89.777 4204 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.75 % Allowed : 15.45 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.56 (0.13), residues: 3724 helix: 4.12 (0.08), residues: 2995 sheet: None (None), residues: 0 loop : -2.36 (0.19), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 37 HIS 0.004 0.001 HIS X 54 PHE 0.037 0.001 PHE F 49 TYR 0.013 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15739.45 seconds wall clock time: 275 minutes 26.29 seconds (16526.29 seconds total)