Starting phenix.real_space_refine on Thu Mar 21 22:55:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4m_9915/03_2024/6k4m_9915_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4m_9915/03_2024/6k4m_9915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4m_9915/03_2024/6k4m_9915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4m_9915/03_2024/6k4m_9915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4m_9915/03_2024/6k4m_9915_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k4m_9915/03_2024/6k4m_9915_updated.pdb" } resolution = 4.5 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= 0.051 sd= 0.650 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 36 7.16 5 S 96 5.16 5 C 19947 2.51 5 N 5375 2.21 5 O 6054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 4": "OD1" <-> "OD2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4": "OD1" <-> "OD2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B ASP 33": "OD1" <-> "OD2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 9": "OE1" <-> "OE2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F ASP 99": "OD1" <-> "OD2" Residue "F ASP 132": "OD1" <-> "OD2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 9": "OE1" <-> "OE2" Residue "E ASP 33": "OD1" <-> "OD2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 4": "OD1" <-> "OD2" Residue "G GLU 9": "OE1" <-> "OE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G ASP 60": "OD1" <-> "OD2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "G TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 4": "OD1" <-> "OD2" Residue "H GLU 9": "OE1" <-> "OE2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H ASP 60": "OD1" <-> "OD2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H ASP 99": "OD1" <-> "OD2" Residue "H ASP 113": "OD1" <-> "OD2" Residue "H ASP 139": "OD1" <-> "OD2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 4": "OD1" <-> "OD2" Residue "I GLU 9": "OE1" <-> "OE2" Residue "I ASP 60": "OD1" <-> "OD2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I GLU 96": "OE1" <-> "OE2" Residue "I ASP 99": "OD1" <-> "OD2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "I ASP 139": "OD1" <-> "OD2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 4": "OD1" <-> "OD2" Residue "J GLU 9": "OE1" <-> "OE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J GLU 85": "OE1" <-> "OE2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J ASP 99": "OD1" <-> "OD2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K ASP 60": "OD1" <-> "OD2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "K GLU 128": "OE1" <-> "OE2" Residue "K ASP 139": "OD1" <-> "OD2" Residue "K TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 4": "OD1" <-> "OD2" Residue "L ASP 33": "OD1" <-> "OD2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L GLU 85": "OE1" <-> "OE2" Residue "L GLU 92": "OE1" <-> "OE2" Residue "L ASP 99": "OD1" <-> "OD2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "L ASP 132": "OD1" <-> "OD2" Residue "L TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 4": "OD1" <-> "OD2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ASP 60": "OD1" <-> "OD2" Residue "M GLU 85": "OE1" <-> "OE2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M ASP 99": "OD1" <-> "OD2" Residue "M GLU 121": "OE1" <-> "OE2" Residue "M TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 4": "OD1" <-> "OD2" Residue "N GLU 85": "OE1" <-> "OE2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "N ASP 99": "OD1" <-> "OD2" Residue "N GLU 121": "OE1" <-> "OE2" Residue "N GLU 127": "OE1" <-> "OE2" Residue "N GLU 128": "OE1" <-> "OE2" Residue "N TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 4": "OD1" <-> "OD2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O GLU 51": "OE1" <-> "OE2" Residue "O GLU 56": "OE1" <-> "OE2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O GLU 92": "OE1" <-> "OE2" Residue "O ASP 99": "OD1" <-> "OD2" Residue "O GLU 121": "OE1" <-> "OE2" Residue "O GLU 128": "OE1" <-> "OE2" Residue "O ASP 132": "OD1" <-> "OD2" Residue "O TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 18": "OE1" <-> "OE2" Residue "P ASP 33": "OD1" <-> "OD2" Residue "P ASP 60": "OD1" <-> "OD2" Residue "P GLU 92": "OE1" <-> "OE2" Residue "P GLU 96": "OE1" <-> "OE2" Residue "P ASP 99": "OD1" <-> "OD2" Residue "P ASP 113": "OD1" <-> "OD2" Residue "P ASP 132": "OD1" <-> "OD2" Residue "P TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 60": "OD1" <-> "OD2" Residue "Q GLU 85": "OE1" <-> "OE2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "Q GLU 96": "OE1" <-> "OE2" Residue "Q ASP 99": "OD1" <-> "OD2" Residue "Q ASP 139": "OD1" <-> "OD2" Residue "Q TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 33": "OD1" <-> "OD2" Residue "R ASP 60": "OD1" <-> "OD2" Residue "R GLU 85": "OE1" <-> "OE2" Residue "R GLU 92": "OE1" <-> "OE2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 121": "OE1" <-> "OE2" Residue "R TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 4": "OD1" <-> "OD2" Residue "S ASP 33": "OD1" <-> "OD2" Residue "S GLU 92": "OE1" <-> "OE2" Residue "S ASP 99": "OD1" <-> "OD2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 9": "OE1" <-> "OE2" Residue "T GLU 92": "OE1" <-> "OE2" Residue "T GLU 96": "OE1" <-> "OE2" Residue "T ASP 113": "OD1" <-> "OD2" Residue "T GLU 121": "OE1" <-> "OE2" Residue "T ASP 139": "OD1" <-> "OD2" Residue "T TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 4": "OD1" <-> "OD2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U ASP 33": "OD1" <-> "OD2" Residue "U GLU 51": "OE1" <-> "OE2" Residue "U GLU 85": "OE1" <-> "OE2" Residue "U GLU 92": "OE1" <-> "OE2" Residue "U ASP 99": "OD1" <-> "OD2" Residue "U GLU 121": "OE1" <-> "OE2" Residue "U ASP 132": "OD1" <-> "OD2" Residue "U ASP 139": "OD1" <-> "OD2" Residue "U TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 4": "OD1" <-> "OD2" Residue "V ASP 50": "OD1" <-> "OD2" Residue "V ASP 60": "OD1" <-> "OD2" Residue "V GLU 85": "OE1" <-> "OE2" Residue "V GLU 92": "OE1" <-> "OE2" Residue "V GLU 96": "OE1" <-> "OE2" Residue "V ASP 99": "OD1" <-> "OD2" Residue "V ASP 113": "OD1" <-> "OD2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "V ASP 139": "OD1" <-> "OD2" Residue "V TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 33": "OD1" <-> "OD2" Residue "W ASP 50": "OD1" <-> "OD2" Residue "W ASP 60": "OD1" <-> "OD2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 96": "OE1" <-> "OE2" Residue "W GLU 121": "OE1" <-> "OE2" Residue "W ASP 132": "OD1" <-> "OD2" Residue "W ASP 139": "OD1" <-> "OD2" Residue "W TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 4": "OD1" <-> "OD2" Residue "X ASP 33": "OD1" <-> "OD2" Residue "X ASP 50": "OD1" <-> "OD2" Residue "X ASP 60": "OD1" <-> "OD2" Residue "X GLU 92": "OE1" <-> "OE2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "X ASP 99": "OD1" <-> "OD2" Residue "X GLU 121": "OE1" <-> "OE2" Residue "X GLU 128": "OE1" <-> "OE2" Residue "X ASP 139": "OD1" <-> "OD2" Residue "X TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 31508 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1301 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.89, per 1000 atoms: 0.50 Number of scatterers: 31508 At special positions: 0 Unit cell: (133.2, 132.09, 133.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 36 26.01 S 96 16.00 O 6054 8.00 N 5375 7.00 C 19947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=31, symmetry=0 Number of additional bonds: simple=31, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.03 Conformation dependent library (CDL) restraints added in 5.9 seconds 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7292 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 0 sheets defined 77.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.49 Creating SS restraints... Processing helix chain 'A' and resid 5 through 34 removed outlier: 3.741A pdb=" N GLN A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 64 removed outlier: 3.793A pdb=" N PHE A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 111 removed outlier: 3.652A pdb=" N PHE A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 144 removed outlier: 3.519A pdb=" N VAL A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR A 133 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.090A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 35 removed outlier: 3.607A pdb=" N GLN B 14 " --> pdb=" O PHE B 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 64 removed outlier: 3.545A pdb=" N PHE B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 57 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 111 removed outlier: 3.675A pdb=" N ASP B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 144 removed outlier: 3.514A pdb=" N ASP B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR B 133 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.855A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 32 removed outlier: 3.792A pdb=" N GLN C 14 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 64 removed outlier: 3.989A pdb=" N PHE C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 56 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG C 61 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 111 removed outlier: 3.717A pdb=" N ARG C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG C 100 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU C 106 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 144 removed outlier: 3.992A pdb=" N VAL C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR C 133 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.990A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 34 removed outlier: 3.797A pdb=" N GLN D 14 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 64 removed outlier: 3.804A pdb=" N ASP D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG D 61 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 111 removed outlier: 3.906A pdb=" N ARG D 91 " --> pdb=" O PHE D 87 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU D 106 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 144 removed outlier: 3.604A pdb=" N ASP D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR D 133 " --> pdb=" O HIS D 129 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 134 " --> pdb=" O HIS D 130 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 152 removed outlier: 4.019A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 32 removed outlier: 3.919A pdb=" N GLN F 14 " --> pdb=" O PHE F 10 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 64 removed outlier: 3.734A pdb=" N PHE F 49 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP F 50 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU F 51 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL F 57 " --> pdb=" O ARG F 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 58 " --> pdb=" O HIS F 54 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 62 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU F 63 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 111 removed outlier: 3.555A pdb=" N ASP F 90 " --> pdb=" O MET F 86 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG F 91 " --> pdb=" O PHE F 87 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU F 92 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG F 100 " --> pdb=" O GLU F 96 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU F 106 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 144 removed outlier: 3.661A pdb=" N ALA F 122 " --> pdb=" O ASN F 118 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR F 133 " --> pdb=" O HIS F 129 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU F 138 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 140 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 152 removed outlier: 4.055A pdb=" N THR F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 34 removed outlier: 3.761A pdb=" N GLN E 14 " --> pdb=" O PHE E 10 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR E 16 " --> pdb=" O ASN E 12 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA E 17 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 64 removed outlier: 3.826A pdb=" N PHE E 49 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU E 51 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 58 " --> pdb=" O HIS E 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU E 63 " --> pdb=" O THR E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 111 removed outlier: 3.899A pdb=" N ARG E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU E 92 " --> pdb=" O GLN E 88 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG E 100 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 144 removed outlier: 3.775A pdb=" N ASP E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 128 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR E 133 " --> pdb=" O HIS E 129 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU E 140 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 152 removed outlier: 4.150A pdb=" N THR E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 34 removed outlier: 3.616A pdb=" N GLN G 14 " --> pdb=" O PHE G 10 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR G 16 " --> pdb=" O ASN G 12 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA G 17 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 64 removed outlier: 3.763A pdb=" N PHE G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU G 51 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL G 57 " --> pdb=" O ARG G 53 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU G 58 " --> pdb=" O HIS G 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU G 63 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 111 removed outlier: 3.855A pdb=" N ARG G 91 " --> pdb=" O PHE G 87 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU G 92 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE G 98 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG G 100 " --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU G 106 " --> pdb=" O ARG G 102 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL G 107 " --> pdb=" O ARG G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 144 removed outlier: 4.065A pdb=" N ASP G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP G 132 " --> pdb=" O GLU G 128 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR G 133 " --> pdb=" O HIS G 129 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 152 removed outlier: 3.859A pdb=" N THR G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 34 removed outlier: 3.710A pdb=" N GLN H 14 " --> pdb=" O PHE H 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA H 17 " --> pdb=" O GLU H 13 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 64 removed outlier: 3.767A pdb=" N PHE H 49 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU H 51 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL H 57 " --> pdb=" O ARG H 53 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU H 63 " --> pdb=" O THR H 59 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 111 removed outlier: 3.833A pdb=" N ARG H 91 " --> pdb=" O PHE H 87 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU H 92 " --> pdb=" O GLN H 88 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE H 98 " --> pdb=" O GLU H 94 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG H 100 " --> pdb=" O GLU H 96 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL H 107 " --> pdb=" O ARG H 103 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 144 removed outlier: 3.719A pdb=" N ASP H 126 " --> pdb=" O ALA H 122 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP H 132 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR H 133 " --> pdb=" O HIS H 129 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU H 140 " --> pdb=" O THR H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 152 removed outlier: 4.013A pdb=" N THR H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 35 removed outlier: 3.670A pdb=" N ALA I 17 " --> pdb=" O GLU I 13 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR I 20 " --> pdb=" O THR I 16 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN I 23 " --> pdb=" O LEU I 19 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 64 removed outlier: 3.754A pdb=" N PHE I 49 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP I 50 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU I 51 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL I 57 " --> pdb=" O ARG I 53 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 58 " --> pdb=" O HIS I 54 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE I 62 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU I 63 " --> pdb=" O THR I 59 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 111 removed outlier: 3.655A pdb=" N ASP I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG I 91 " --> pdb=" O PHE I 87 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU I 92 " --> pdb=" O GLN I 88 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE I 98 " --> pdb=" O GLU I 94 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP I 99 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE I 105 " --> pdb=" O LEU I 101 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL I 107 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 128 removed outlier: 3.558A pdb=" N VAL I 119 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 126 " --> pdb=" O ALA I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 144 removed outlier: 3.746A pdb=" N ASP I 139 " --> pdb=" O GLU I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 152 removed outlier: 3.863A pdb=" N THR I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 35 removed outlier: 3.731A pdb=" N GLN J 14 " --> pdb=" O PHE J 10 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA J 17 " --> pdb=" O GLU J 13 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR J 20 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN J 23 " --> pdb=" O LEU J 19 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS J 34 " --> pdb=" O LYS J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 64 removed outlier: 3.677A pdb=" N PHE J 49 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP J 50 " --> pdb=" O ALA J 46 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU J 51 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL J 57 " --> pdb=" O ARG J 53 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU J 58 " --> pdb=" O HIS J 54 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG J 61 " --> pdb=" O VAL J 57 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE J 62 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU J 63 " --> pdb=" O THR J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 110 removed outlier: 3.883A pdb=" N ASP J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG J 91 " --> pdb=" O PHE J 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU J 92 " --> pdb=" O GLN J 88 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE J 98 " --> pdb=" O GLU J 94 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP J 99 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG J 100 " --> pdb=" O GLU J 96 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE J 105 " --> pdb=" O LEU J 101 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU J 106 " --> pdb=" O ARG J 102 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL J 107 " --> pdb=" O ARG J 103 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 142 removed outlier: 3.504A pdb=" N ALA J 122 " --> pdb=" O ASN J 118 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP J 132 " --> pdb=" O GLU J 128 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR J 133 " --> pdb=" O HIS J 129 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU J 140 " --> pdb=" O THR J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 152 removed outlier: 3.859A pdb=" N THR J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 35 removed outlier: 3.809A pdb=" N GLN K 14 " --> pdb=" O PHE K 10 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN K 23 " --> pdb=" O LEU K 19 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 64 removed outlier: 3.636A pdb=" N PHE K 49 " --> pdb=" O ARG K 45 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU K 51 " --> pdb=" O GLU K 47 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL K 57 " --> pdb=" O ARG K 53 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE K 62 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU K 63 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.844A pdb=" N ARG K 91 " --> pdb=" O PHE K 87 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU K 92 " --> pdb=" O GLN K 88 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE K 98 " --> pdb=" O GLU K 94 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP K 99 " --> pdb=" O LEU K 95 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG K 100 " --> pdb=" O GLU K 96 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE K 105 " --> pdb=" O LEU K 101 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU K 106 " --> pdb=" O ARG K 102 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL K 107 " --> pdb=" O ARG K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 128 removed outlier: 4.126A pdb=" N ASP K 126 " --> pdb=" O ALA K 122 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU K 127 " --> pdb=" O ILE K 123 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 144 removed outlier: 3.637A pdb=" N ASP K 139 " --> pdb=" O GLU K 135 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU K 144 " --> pdb=" O LEU K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 152 removed outlier: 3.970A pdb=" N THR K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 35 removed outlier: 3.606A pdb=" N PHE L 10 " --> pdb=" O GLU L 6 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN L 23 " --> pdb=" O LEU L 19 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 64 removed outlier: 3.601A pdb=" N PHE L 49 " --> pdb=" O ARG L 45 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP L 50 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU L 51 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU L 58 " --> pdb=" O HIS L 54 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU L 63 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 111 removed outlier: 3.792A pdb=" N ARG L 91 " --> pdb=" O PHE L 87 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU L 92 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG L 100 " --> pdb=" O GLU L 96 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE L 105 " --> pdb=" O LEU L 101 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU L 106 " --> pdb=" O ARG L 102 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 144 removed outlier: 3.621A pdb=" N VAL L 119 " --> pdb=" O THR L 115 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP L 126 " --> pdb=" O ALA L 122 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU L 127 " --> pdb=" O ILE L 123 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS L 129 " --> pdb=" O ALA L 125 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR L 133 " --> pdb=" O HIS L 129 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP L 139 " --> pdb=" O GLU L 135 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU L 140 " --> pdb=" O THR L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 152 removed outlier: 3.934A pdb=" N THR L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 34 removed outlier: 3.632A pdb=" N PHE M 10 " --> pdb=" O GLU M 6 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN M 14 " --> pdb=" O PHE M 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA M 17 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN M 23 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 64 removed outlier: 3.919A pdb=" N ASP M 50 " --> pdb=" O ALA M 46 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU M 51 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL M 57 " --> pdb=" O ARG M 53 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE M 62 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU M 63 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 111 removed outlier: 3.899A pdb=" N ARG M 91 " --> pdb=" O PHE M 87 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU M 92 " --> pdb=" O GLN M 88 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP M 99 " --> pdb=" O LEU M 95 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG M 100 " --> pdb=" O GLU M 96 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE M 105 " --> pdb=" O LEU M 101 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU M 106 " --> pdb=" O ARG M 102 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL M 107 " --> pdb=" O ARG M 103 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 144 removed outlier: 3.530A pdb=" N ASP M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU M 127 " --> pdb=" O ILE M 123 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP M 132 " --> pdb=" O GLU M 128 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR M 133 " --> pdb=" O HIS M 129 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP M 139 " --> pdb=" O GLU M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 152 removed outlier: 3.857A pdb=" N THR M 152 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 34 removed outlier: 3.616A pdb=" N PHE N 10 " --> pdb=" O GLU N 6 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA N 17 " --> pdb=" O GLU N 13 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN N 23 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 64 removed outlier: 3.981A pdb=" N PHE N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP N 50 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU N 51 " --> pdb=" O GLU N 47 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL N 57 " --> pdb=" O ARG N 53 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU N 58 " --> pdb=" O HIS N 54 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE N 62 " --> pdb=" O LEU N 58 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU N 63 " --> pdb=" O THR N 59 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 111 removed outlier: 3.705A pdb=" N ARG N 91 " --> pdb=" O PHE N 87 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU N 92 " --> pdb=" O GLN N 88 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE N 98 " --> pdb=" O GLU N 94 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP N 99 " --> pdb=" O LEU N 95 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU N 106 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL N 107 " --> pdb=" O ARG N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 144 removed outlier: 3.869A pdb=" N ASP N 126 " --> pdb=" O ALA N 122 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP N 132 " --> pdb=" O GLU N 128 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR N 133 " --> pdb=" O HIS N 129 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU N 134 " --> pdb=" O HIS N 130 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP N 139 " --> pdb=" O GLU N 135 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU N 140 " --> pdb=" O THR N 136 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU N 144 " --> pdb=" O LEU N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 152 removed outlier: 4.054A pdb=" N THR N 152 " --> pdb=" O LEU N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 34 removed outlier: 3.542A pdb=" N GLN O 14 " --> pdb=" O PHE O 10 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA O 17 " --> pdb=" O GLU O 13 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE O 22 " --> pdb=" O GLU O 18 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN O 24 " --> pdb=" O THR O 20 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 64 removed outlier: 3.881A pdb=" N PHE O 49 " --> pdb=" O ARG O 45 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP O 50 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU O 51 " --> pdb=" O GLU O 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU O 56 " --> pdb=" O MET O 52 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL O 57 " --> pdb=" O ARG O 53 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU O 58 " --> pdb=" O HIS O 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU O 63 " --> pdb=" O THR O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 111 removed outlier: 3.726A pdb=" N PHE O 87 " --> pdb=" O VAL O 83 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG O 91 " --> pdb=" O PHE O 87 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU O 92 " --> pdb=" O GLN O 88 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE O 98 " --> pdb=" O GLU O 94 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP O 99 " --> pdb=" O LEU O 95 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG O 100 " --> pdb=" O GLU O 96 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU O 106 " --> pdb=" O ARG O 102 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL O 107 " --> pdb=" O ARG O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 144 removed outlier: 3.911A pdb=" N ASP O 126 " --> pdb=" O ALA O 122 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP O 132 " --> pdb=" O GLU O 128 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR O 133 " --> pdb=" O HIS O 129 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU O 134 " --> pdb=" O HIS O 130 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP O 139 " --> pdb=" O GLU O 135 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU O 144 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 152 removed outlier: 4.070A pdb=" N THR O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 35 removed outlier: 3.820A pdb=" N GLN P 14 " --> pdb=" O PHE P 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP P 33 " --> pdb=" O ALA P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 64 removed outlier: 3.599A pdb=" N PHE P 49 " --> pdb=" O ARG P 45 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU P 51 " --> pdb=" O GLU P 47 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU P 56 " --> pdb=" O MET P 52 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL P 57 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU P 58 " --> pdb=" O HIS P 54 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU P 63 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU P 64 " --> pdb=" O ASP P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 111 removed outlier: 3.557A pdb=" N ASP P 90 " --> pdb=" O MET P 86 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU P 92 " --> pdb=" O GLN P 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE P 98 " --> pdb=" O GLU P 94 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG P 100 " --> pdb=" O GLU P 96 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE P 105 " --> pdb=" O LEU P 101 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU P 106 " --> pdb=" O ARG P 102 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL P 107 " --> pdb=" O ARG P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 144 removed outlier: 4.040A pdb=" N ASP P 126 " --> pdb=" O ALA P 122 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU P 127 " --> pdb=" O ILE P 123 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP P 132 " --> pdb=" O GLU P 128 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR P 133 " --> pdb=" O HIS P 129 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP P 139 " --> pdb=" O GLU P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 152 removed outlier: 3.881A pdb=" N THR P 152 " --> pdb=" O LEU P 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 34 removed outlier: 3.524A pdb=" N PHE Q 10 " --> pdb=" O GLU Q 6 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN Q 14 " --> pdb=" O PHE Q 10 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA Q 21 " --> pdb=" O ALA Q 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE Q 22 " --> pdb=" O GLU Q 18 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 64 removed outlier: 3.734A pdb=" N PHE Q 49 " --> pdb=" O ARG Q 45 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP Q 50 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU Q 51 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET Q 52 " --> pdb=" O SER Q 48 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU Q 63 " --> pdb=" O THR Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 111 removed outlier: 3.905A pdb=" N ARG Q 91 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU Q 92 " --> pdb=" O GLN Q 88 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE Q 98 " --> pdb=" O GLU Q 94 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG Q 100 " --> pdb=" O GLU Q 96 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE Q 105 " --> pdb=" O LEU Q 101 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU Q 106 " --> pdb=" O ARG Q 102 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 144 removed outlier: 3.506A pdb=" N VAL Q 119 " --> pdb=" O THR Q 115 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP Q 126 " --> pdb=" O ALA Q 122 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP Q 132 " --> pdb=" O GLU Q 128 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR Q 133 " --> pdb=" O HIS Q 129 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP Q 139 " --> pdb=" O GLU Q 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 152 removed outlier: 4.064A pdb=" N THR Q 152 " --> pdb=" O LEU Q 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 34 removed outlier: 3.608A pdb=" N PHE R 10 " --> pdb=" O GLU R 6 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN R 14 " --> pdb=" O PHE R 10 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA R 17 " --> pdb=" O GLU R 13 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR R 20 " --> pdb=" O THR R 16 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 64 removed outlier: 3.502A pdb=" N PHE R 49 " --> pdb=" O ARG R 45 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL R 57 " --> pdb=" O ARG R 53 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG R 61 " --> pdb=" O VAL R 57 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE R 62 " --> pdb=" O LEU R 58 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU R 64 " --> pdb=" O ASP R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 111 removed outlier: 3.773A pdb=" N ASP R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG R 91 " --> pdb=" O PHE R 87 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU R 92 " --> pdb=" O GLN R 88 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE R 98 " --> pdb=" O GLU R 94 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP R 99 " --> pdb=" O LEU R 95 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG R 100 " --> pdb=" O GLU R 96 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU R 106 " --> pdb=" O ARG R 102 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL R 107 " --> pdb=" O ARG R 103 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS R 111 " --> pdb=" O VAL R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 144 removed outlier: 3.909A pdb=" N ASP R 126 " --> pdb=" O ALA R 122 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS R 129 " --> pdb=" O ALA R 125 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP R 132 " --> pdb=" O GLU R 128 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR R 133 " --> pdb=" O HIS R 129 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP R 139 " --> pdb=" O GLU R 135 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 152 removed outlier: 3.978A pdb=" N THR R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 34 removed outlier: 3.829A pdb=" N GLN S 14 " --> pdb=" O PHE S 10 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA S 17 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR S 20 " --> pdb=" O THR S 16 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 64 removed outlier: 3.945A pdb=" N PHE S 49 " --> pdb=" O ARG S 45 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP S 50 " --> pdb=" O ALA S 46 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU S 51 " --> pdb=" O GLU S 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU S 56 " --> pdb=" O MET S 52 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL S 57 " --> pdb=" O ARG S 53 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG S 61 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE S 62 " --> pdb=" O LEU S 58 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU S 63 " --> pdb=" O THR S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 111 removed outlier: 3.763A pdb=" N ASP S 90 " --> pdb=" O MET S 86 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG S 91 " --> pdb=" O PHE S 87 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU S 92 " --> pdb=" O GLN S 88 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE S 98 " --> pdb=" O GLU S 94 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP S 99 " --> pdb=" O LEU S 95 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG S 100 " --> pdb=" O GLU S 96 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE S 105 " --> pdb=" O LEU S 101 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU S 106 " --> pdb=" O ARG S 102 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL S 107 " --> pdb=" O ARG S 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 144 removed outlier: 3.549A pdb=" N VAL S 119 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA S 122 " --> pdb=" O ASN S 118 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP S 132 " --> pdb=" O GLU S 128 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR S 133 " --> pdb=" O HIS S 129 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP S 139 " --> pdb=" O GLU S 135 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU S 144 " --> pdb=" O LEU S 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 152 removed outlier: 4.022A pdb=" N THR S 152 " --> pdb=" O LEU S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 34 removed outlier: 3.777A pdb=" N ALA T 17 " --> pdb=" O GLU T 13 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR T 20 " --> pdb=" O THR T 16 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 64 removed outlier: 3.924A pdb=" N PHE T 49 " --> pdb=" O ARG T 45 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP T 50 " --> pdb=" O ALA T 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU T 51 " --> pdb=" O GLU T 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL T 57 " --> pdb=" O ARG T 53 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU T 58 " --> pdb=" O HIS T 54 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG T 61 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE T 62 " --> pdb=" O LEU T 58 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU T 63 " --> pdb=" O THR T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 111 removed outlier: 3.884A pdb=" N PHE T 87 " --> pdb=" O VAL T 83 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG T 91 " --> pdb=" O PHE T 87 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU T 92 " --> pdb=" O GLN T 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE T 98 " --> pdb=" O GLU T 94 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP T 99 " --> pdb=" O LEU T 95 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG T 100 " --> pdb=" O GLU T 96 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU T 106 " --> pdb=" O ARG T 102 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL T 107 " --> pdb=" O ARG T 103 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS T 111 " --> pdb=" O VAL T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 144 removed outlier: 3.823A pdb=" N ASP T 126 " --> pdb=" O ALA T 122 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP T 132 " --> pdb=" O GLU T 128 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR T 133 " --> pdb=" O HIS T 129 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP T 139 " --> pdb=" O GLU T 135 " (cutoff:3.500A) Processing helix chain 'T' and resid 147 through 152 removed outlier: 4.049A pdb=" N THR T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 35 removed outlier: 3.642A pdb=" N GLN U 14 " --> pdb=" O PHE U 10 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR U 20 " --> pdb=" O THR U 16 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE U 22 " --> pdb=" O GLU U 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS U 34 " --> pdb=" O LYS U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 64 removed outlier: 3.530A pdb=" N PHE U 49 " --> pdb=" O ARG U 45 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU U 51 " --> pdb=" O GLU U 47 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL U 57 " --> pdb=" O ARG U 53 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU U 58 " --> pdb=" O HIS U 54 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU U 63 " --> pdb=" O THR U 59 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU U 64 " --> pdb=" O ASP U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 111 removed outlier: 3.660A pdb=" N ASP U 90 " --> pdb=" O MET U 86 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG U 91 " --> pdb=" O PHE U 87 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU U 92 " --> pdb=" O GLN U 88 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE U 98 " --> pdb=" O GLU U 94 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP U 99 " --> pdb=" O LEU U 95 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG U 100 " --> pdb=" O GLU U 96 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU U 106 " --> pdb=" O ARG U 102 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL U 107 " --> pdb=" O ARG U 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 115 through 144 removed outlier: 3.638A pdb=" N ASP U 126 " --> pdb=" O ALA U 122 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP U 132 " --> pdb=" O GLU U 128 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR U 133 " --> pdb=" O HIS U 129 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU U 134 " --> pdb=" O HIS U 130 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU U 144 " --> pdb=" O LEU U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 152 removed outlier: 3.895A pdb=" N THR U 152 " --> pdb=" O LEU U 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 32 removed outlier: 3.613A pdb=" N PHE V 10 " --> pdb=" O GLU V 6 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA V 17 " --> pdb=" O GLU V 13 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR V 20 " --> pdb=" O THR V 16 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN V 23 " --> pdb=" O LEU V 19 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS V 28 " --> pdb=" O GLN V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 64 removed outlier: 3.555A pdb=" N PHE V 49 " --> pdb=" O ARG V 45 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP V 50 " --> pdb=" O ALA V 46 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU V 51 " --> pdb=" O GLU V 47 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU V 58 " --> pdb=" O HIS V 54 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE V 62 " --> pdb=" O LEU V 58 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU V 63 " --> pdb=" O THR V 59 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU V 64 " --> pdb=" O ASP V 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 83 through 111 removed outlier: 3.708A pdb=" N ARG V 91 " --> pdb=" O PHE V 87 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU V 92 " --> pdb=" O GLN V 88 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE V 98 " --> pdb=" O GLU V 94 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP V 99 " --> pdb=" O LEU V 95 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG V 100 " --> pdb=" O GLU V 96 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU V 106 " --> pdb=" O ARG V 102 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL V 107 " --> pdb=" O ARG V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 115 through 144 removed outlier: 3.605A pdb=" N VAL V 119 " --> pdb=" O THR V 115 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP V 132 " --> pdb=" O GLU V 128 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR V 133 " --> pdb=" O HIS V 129 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP V 139 " --> pdb=" O GLU V 135 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU V 144 " --> pdb=" O LEU V 140 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 152 removed outlier: 3.970A pdb=" N THR V 152 " --> pdb=" O LEU V 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 35 removed outlier: 3.575A pdb=" N PHE W 10 " --> pdb=" O GLU W 6 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR W 20 " --> pdb=" O THR W 16 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA W 21 " --> pdb=" O ALA W 17 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN W 23 " --> pdb=" O LEU W 19 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS W 28 " --> pdb=" O GLN W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 64 removed outlier: 3.695A pdb=" N PHE W 49 " --> pdb=" O ARG W 45 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP W 50 " --> pdb=" O ALA W 46 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU W 51 " --> pdb=" O GLU W 47 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU W 56 " --> pdb=" O MET W 52 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL W 57 " --> pdb=" O ARG W 53 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU W 58 " --> pdb=" O HIS W 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE W 62 " --> pdb=" O LEU W 58 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU W 63 " --> pdb=" O THR W 59 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU W 64 " --> pdb=" O ASP W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 111 removed outlier: 3.846A pdb=" N ASP W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG W 91 " --> pdb=" O PHE W 87 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU W 92 " --> pdb=" O GLN W 88 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE W 98 " --> pdb=" O GLU W 94 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP W 99 " --> pdb=" O LEU W 95 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG W 100 " --> pdb=" O GLU W 96 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU W 106 " --> pdb=" O ARG W 102 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL W 107 " --> pdb=" O ARG W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 115 through 144 removed outlier: 3.518A pdb=" N VAL W 119 " --> pdb=" O THR W 115 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP W 126 " --> pdb=" O ALA W 122 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP W 132 " --> pdb=" O GLU W 128 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR W 133 " --> pdb=" O HIS W 129 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU W 134 " --> pdb=" O HIS W 130 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP W 139 " --> pdb=" O GLU W 135 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU W 144 " --> pdb=" O LEU W 140 " (cutoff:3.500A) Processing helix chain 'W' and resid 146 through 152 removed outlier: 3.818A pdb=" N THR W 152 " --> pdb=" O LEU W 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 34 removed outlier: 3.602A pdb=" N PHE X 10 " --> pdb=" O GLU X 6 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA X 17 " --> pdb=" O GLU X 13 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR X 20 " --> pdb=" O THR X 16 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN X 23 " --> pdb=" O LEU X 19 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS X 28 " --> pdb=" O GLN X 24 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP X 33 " --> pdb=" O ALA X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 64 removed outlier: 3.760A pdb=" N PHE X 49 " --> pdb=" O ARG X 45 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP X 50 " --> pdb=" O ALA X 46 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL X 57 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU X 58 " --> pdb=" O HIS X 54 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG X 61 " --> pdb=" O VAL X 57 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE X 62 " --> pdb=" O LEU X 58 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU X 63 " --> pdb=" O THR X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 111 removed outlier: 3.894A pdb=" N ARG X 91 " --> pdb=" O PHE X 87 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU X 92 " --> pdb=" O GLN X 88 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE X 98 " --> pdb=" O GLU X 94 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG X 100 " --> pdb=" O GLU X 96 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE X 105 " --> pdb=" O LEU X 101 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU X 106 " --> pdb=" O ARG X 102 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL X 107 " --> pdb=" O ARG X 103 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 144 removed outlier: 3.547A pdb=" N ALA X 122 " --> pdb=" O ASN X 118 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP X 126 " --> pdb=" O ALA X 122 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP X 132 " --> pdb=" O GLU X 128 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR X 133 " --> pdb=" O HIS X 129 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP X 139 " --> pdb=" O GLU X 135 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU X 144 " --> pdb=" O LEU X 140 " (cutoff:3.500A) Processing helix chain 'X' and resid 146 through 152 removed outlier: 3.837A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 1785 hydrogen bonds defined for protein. 5355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.78 Time building geometry restraints manager: 14.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 13390 1.40 - 1.58: 18442 1.58 - 1.76: 0 1.76 - 1.94: 192 1.94 - 2.12: 48 Bond restraints: 32072 Sorted by residual: bond pdb=" C VAL D 153 " pdb=" N ILE D 154 " ideal model delta sigma weight residual 1.329 1.310 0.019 1.07e-02 8.73e+03 3.24e+00 bond pdb=" C VAL U 153 " pdb=" N ILE U 154 " ideal model delta sigma weight residual 1.327 1.310 0.017 9.50e-03 1.11e+04 3.19e+00 bond pdb=" C ASP J 113 " pdb=" N ILE J 114 " ideal model delta sigma weight residual 1.332 1.316 0.016 1.16e-02 7.43e+03 1.96e+00 bond pdb=" CA LEU V 65 " pdb=" C LEU V 65 " ideal model delta sigma weight residual 1.523 1.503 0.019 1.41e-02 5.03e+03 1.87e+00 bond pdb=" C VAL W 153 " pdb=" N ILE W 154 " ideal model delta sigma weight residual 1.330 1.313 0.017 1.26e-02 6.30e+03 1.81e+00 ... (remaining 32067 not shown) Histogram of bond angle deviations from ideal: 86.07 - 104.64: 271 104.64 - 123.20: 41694 123.20 - 141.76: 1511 141.76 - 160.33: 0 160.33 - 178.89: 24 Bond angle restraints: 43500 Sorted by residual: angle pdb=" N VAL P 153 " pdb=" CA VAL P 153 " pdb=" C VAL P 153 " ideal model delta sigma weight residual 113.10 107.69 5.41 9.70e-01 1.06e+00 3.11e+01 angle pdb=" N VAL K 153 " pdb=" CA VAL K 153 " pdb=" C VAL K 153 " ideal model delta sigma weight residual 113.22 107.71 5.51 1.23e+00 6.61e-01 2.00e+01 angle pdb=" N ILE D 114 " pdb=" CA ILE D 114 " pdb=" C ILE D 114 " ideal model delta sigma weight residual 112.96 108.99 3.97 1.00e+00 1.00e+00 1.58e+01 angle pdb=" N VAL L 153 " pdb=" CA VAL L 153 " pdb=" C VAL L 153 " ideal model delta sigma weight residual 112.29 108.66 3.63 9.40e-01 1.13e+00 1.49e+01 angle pdb=" N LYS T 111 " pdb=" CA LYS T 111 " pdb=" C LYS T 111 " ideal model delta sigma weight residual 110.44 114.20 -3.76 1.20e+00 6.94e-01 9.82e+00 ... (remaining 43495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16493 17.96 - 35.92: 2160 35.92 - 53.88: 293 53.88 - 71.84: 161 71.84 - 89.79: 73 Dihedral angle restraints: 19180 sinusoidal: 8002 harmonic: 11178 Sorted by residual: dihedral pdb=" CA LYS M 111 " pdb=" C LYS M 111 " pdb=" N HIS M 112 " pdb=" CA HIS M 112 " ideal model delta harmonic sigma weight residual 180.00 146.97 33.03 0 5.00e+00 4.00e-02 4.36e+01 dihedral pdb=" CA LYS J 111 " pdb=" C LYS J 111 " pdb=" N HIS J 112 " pdb=" CA HIS J 112 " ideal model delta harmonic sigma weight residual 180.00 147.35 32.65 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA TRP J 37 " pdb=" C TRP J 37 " pdb=" N THR J 38 " pdb=" CA THR J 38 " ideal model delta harmonic sigma weight residual -180.00 -147.41 -32.59 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 19177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3546 0.044 - 0.088: 988 0.088 - 0.132: 237 0.132 - 0.177: 49 0.177 - 0.221: 9 Chirality restraints: 4829 Sorted by residual: chirality pdb=" CB ILE S 98 " pdb=" CA ILE S 98 " pdb=" CG1 ILE S 98 " pdb=" CG2 ILE S 98 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL P 153 " pdb=" CA VAL P 153 " pdb=" CG1 VAL P 153 " pdb=" CG2 VAL P 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CG LEU T 58 " pdb=" CB LEU T 58 " pdb=" CD1 LEU T 58 " pdb=" CD2 LEU T 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 4826 not shown) Planarity restraints: 5615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 150 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C LEU A 150 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 150 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 151 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 120 " -0.011 2.00e-02 2.50e+03 1.25e-02 2.75e+00 pdb=" CG PHE F 120 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE F 120 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE F 120 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE F 120 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 120 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 120 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE W 114 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C ILE W 114 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE W 114 " 0.010 2.00e-02 2.50e+03 pdb=" N THR W 115 " 0.009 2.00e-02 2.50e+03 ... (remaining 5612 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8839 2.79 - 3.32: 33421 3.32 - 3.84: 55026 3.84 - 4.37: 66194 4.37 - 4.90: 98221 Nonbonded interactions: 261701 Sorted by model distance: nonbonded pdb=" OD2 ASP R 113 " pdb=" OG SER R 116 " model vdw 2.258 2.440 nonbonded pdb=" OD2 ASP B 113 " pdb=" OG SER B 116 " model vdw 2.262 2.440 nonbonded pdb=" OD2 ASP W 113 " pdb=" OG SER W 116 " model vdw 2.270 2.440 nonbonded pdb=" OE1 GLN X 137 " pdb=" OH TYR X 149 " model vdw 2.272 2.440 nonbonded pdb=" OE1 GLN E 137 " pdb=" OH TYR E 149 " model vdw 2.273 2.440 ... (remaining 261696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 157) selection = (chain 'B' and resid 1 through 157) selection = (chain 'C' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'D' and resid 1 through 157) selection = (chain 'E' and resid 1 through 157) selection = (chain 'F' and resid 1 through 157) selection = (chain 'G' and resid 1 through 157) selection = (chain 'H' and resid 1 through 157) selection = (chain 'I' and resid 1 through 157) selection = (chain 'J' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'K' and resid 1 through 157) selection = (chain 'L' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'M' and resid 1 through 157) selection = (chain 'N' and resid 1 through 157) selection = (chain 'O' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'P' and resid 1 through 157) selection = (chain 'Q' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'R' and resid 1 through 157) selection = (chain 'S' and resid 1 through 157) selection = (chain 'T' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'U' and resid 1 through 157) selection = (chain 'V' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'W' and resid 1 through 157) selection = (chain 'X' and resid 1 through 157) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 group one per residue 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.780 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 80.370 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.140 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 : 0.006 0.074 32072 Z= 0.377 Angle : 1.009 12.419 43500 Z= 0.563 Chirality : 0.045 0.221 4829 Planarity : 0.004 0.031 5615 Dihedral : 17.743 89.795 11888 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.54 % Allowed : 12.11 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.61 (0.09), residues: 3742 helix: -2.80 (0.06), residues: 2792 sheet: None (None), residues: 0 loop : -3.11 (0.15), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP L 37 HIS 0.008 0.002 HIS R 130 PHE 0.029 0.002 PHE F 120 TYR 0.017 0.002 TYR J 71 ARG 0.007 0.001 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1683 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1665 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9387 (mpp) cc_final: 0.8412 (tmm) REVERT: A 2 GLN cc_start: 0.9483 (mt0) cc_final: 0.9130 (pm20) REVERT: A 26 PHE cc_start: 0.9805 (t80) cc_final: 0.9396 (t80) REVERT: A 27 LEU cc_start: 0.9546 (mt) cc_final: 0.9183 (mt) REVERT: A 32 GLN cc_start: 0.9466 (pt0) cc_final: 0.9264 (pt0) REVERT: A 120 PHE cc_start: 0.9523 (m-10) cc_final: 0.9082 (m-10) REVERT: A 155 GLU cc_start: 0.9335 (tm-30) cc_final: 0.8707 (pm20) REVERT: A 156 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8117 (mt0) REVERT: B 2 GLN cc_start: 0.9530 (mt0) cc_final: 0.9253 (pm20) REVERT: B 26 PHE cc_start: 0.9750 (t80) cc_final: 0.9256 (t80) REVERT: B 30 LYS cc_start: 0.9677 (mmmt) cc_final: 0.9424 (mmmt) REVERT: B 34 HIS cc_start: 0.9551 (t70) cc_final: 0.9095 (t70) REVERT: B 35 LYS cc_start: 0.9784 (mttm) cc_final: 0.9552 (mmmm) REVERT: B 71 TYR cc_start: 0.9243 (m-10) cc_final: 0.8575 (m-80) REVERT: B 108 MET cc_start: 0.9655 (ptm) cc_final: 0.9359 (ppp) REVERT: B 111 LYS cc_start: 0.9551 (mmmt) cc_final: 0.9323 (mmmt) REVERT: B 120 PHE cc_start: 0.9365 (m-10) cc_final: 0.9152 (m-80) REVERT: B 154 ILE cc_start: 0.9585 (pt) cc_final: 0.9293 (mm) REVERT: C 26 PHE cc_start: 0.9795 (t80) cc_final: 0.9480 (t80) REVERT: C 58 LEU cc_start: 0.9552 (mt) cc_final: 0.9073 (mt) REVERT: C 91 ARG cc_start: 0.8610 (ttt-90) cc_final: 0.8379 (tpt-90) REVERT: C 100 ARG cc_start: 0.9629 (ttm110) cc_final: 0.9423 (ptm160) REVERT: C 108 MET cc_start: 0.9569 (mtp) cc_final: 0.9278 (mtp) REVERT: C 120 PHE cc_start: 0.9448 (m-80) cc_final: 0.8891 (m-80) REVERT: C 123 ILE cc_start: 0.9368 (tt) cc_final: 0.9153 (tt) REVERT: D 1 MET cc_start: 0.9287 (mmp) cc_final: 0.8308 (tmm) REVERT: D 2 GLN cc_start: 0.9555 (mt0) cc_final: 0.9129 (pm20) REVERT: D 24 GLN cc_start: 0.9582 (tt0) cc_final: 0.9380 (tt0) REVERT: D 26 PHE cc_start: 0.9787 (t80) cc_final: 0.9521 (t80) REVERT: D 35 LYS cc_start: 0.9784 (mttm) cc_final: 0.9537 (mmmm) REVERT: D 108 MET cc_start: 0.9509 (ttt) cc_final: 0.8574 (ttt) REVERT: D 114 ILE cc_start: 0.9306 (mm) cc_final: 0.9076 (mm) REVERT: D 116 SER cc_start: 0.9719 (m) cc_final: 0.9104 (p) REVERT: D 120 PHE cc_start: 0.9291 (m-10) cc_final: 0.8820 (m-80) REVERT: F 9 GLU cc_start: 0.9715 (tp30) cc_final: 0.9511 (tp30) REVERT: F 22 ILE cc_start: 0.9801 (mt) cc_final: 0.9583 (mm) REVERT: F 23 ASN cc_start: 0.9653 (m-40) cc_final: 0.9402 (m110) REVERT: F 26 PHE cc_start: 0.9788 (t80) cc_final: 0.9464 (t80) REVERT: F 71 TYR cc_start: 0.9455 (m-10) cc_final: 0.8979 (m-80) REVERT: F 111 LYS cc_start: 0.9517 (mmmt) cc_final: 0.9254 (mmmt) REVERT: F 120 PHE cc_start: 0.9351 (m-10) cc_final: 0.9148 (m-10) REVERT: E 26 PHE cc_start: 0.9795 (t80) cc_final: 0.9344 (t80) REVERT: E 27 LEU cc_start: 0.9548 (mt) cc_final: 0.9180 (mt) REVERT: E 58 LEU cc_start: 0.9645 (mt) cc_final: 0.9297 (mt) REVERT: E 86 MET cc_start: 0.9665 (mtm) cc_final: 0.9408 (mpp) REVERT: E 111 LYS cc_start: 0.9602 (mmmt) cc_final: 0.9391 (mmmt) REVERT: E 120 PHE cc_start: 0.9556 (m-10) cc_final: 0.9321 (m-80) REVERT: E 139 ASP cc_start: 0.9529 (m-30) cc_final: 0.9005 (p0) REVERT: G 1 MET cc_start: 0.9243 (mpp) cc_final: 0.8948 (mpp) REVERT: G 2 GLN cc_start: 0.9498 (mt0) cc_final: 0.9176 (pm20) REVERT: G 8 ILE cc_start: 0.9435 (mm) cc_final: 0.9222 (mm) REVERT: G 23 ASN cc_start: 0.9720 (m-40) cc_final: 0.9382 (t0) REVERT: G 26 PHE cc_start: 0.9667 (t80) cc_final: 0.9386 (t80) REVERT: G 27 LEU cc_start: 0.9593 (mt) cc_final: 0.9168 (mm) REVERT: G 56 GLU cc_start: 0.9589 (tt0) cc_final: 0.9387 (pp20) REVERT: G 100 ARG cc_start: 0.9463 (ttp-110) cc_final: 0.9183 (ptm160) REVERT: G 120 PHE cc_start: 0.9476 (m-10) cc_final: 0.9160 (m-80) REVERT: G 154 ILE cc_start: 0.9526 (pt) cc_final: 0.9248 (mt) REVERT: H 10 PHE cc_start: 0.9580 (m-10) cc_final: 0.9370 (m-80) REVERT: H 26 PHE cc_start: 0.9753 (t80) cc_final: 0.9333 (t80) REVERT: H 71 TYR cc_start: 0.9419 (m-80) cc_final: 0.8690 (m-80) REVERT: H 99 ASP cc_start: 0.9383 (p0) cc_final: 0.9001 (p0) REVERT: H 100 ARG cc_start: 0.9449 (mmt180) cc_final: 0.9238 (mmm160) REVERT: H 111 LYS cc_start: 0.9538 (mmmt) cc_final: 0.9286 (mmmt) REVERT: H 120 PHE cc_start: 0.9217 (m-10) cc_final: 0.9004 (m-80) REVERT: H 154 ILE cc_start: 0.9477 (pt) cc_final: 0.9240 (mp) REVERT: I 2 GLN cc_start: 0.9568 (mt0) cc_final: 0.9229 (mm-40) REVERT: I 24 GLN cc_start: 0.9580 (tt0) cc_final: 0.9280 (tm-30) REVERT: I 26 PHE cc_start: 0.9793 (t80) cc_final: 0.9513 (t80) REVERT: J 1 MET cc_start: 0.9439 (mpp) cc_final: 0.8827 (mpp) REVERT: J 2 GLN cc_start: 0.9496 (mt0) cc_final: 0.9206 (mm-40) REVERT: J 26 PHE cc_start: 0.9722 (t80) cc_final: 0.9459 (t80) REVERT: J 108 MET cc_start: 0.9503 (ptm) cc_final: 0.9215 (ptm) REVERT: J 120 PHE cc_start: 0.9430 (m-10) cc_final: 0.9067 (m-80) REVERT: J 123 ILE cc_start: 0.9630 (pt) cc_final: 0.9411 (tt) REVERT: K 2 GLN cc_start: 0.9571 (mt0) cc_final: 0.9359 (pm20) REVERT: K 10 PHE cc_start: 0.9535 (m-10) cc_final: 0.9325 (m-80) REVERT: K 22 ILE cc_start: 0.9799 (mt) cc_final: 0.9548 (tt) REVERT: K 23 ASN cc_start: 0.9740 (m-40) cc_final: 0.9367 (m-40) REVERT: K 26 PHE cc_start: 0.9736 (t80) cc_final: 0.9296 (t80) REVERT: K 30 LYS cc_start: 0.9711 (mmmt) cc_final: 0.9441 (mptt) REVERT: K 58 LEU cc_start: 0.9734 (mt) cc_final: 0.9533 (mt) REVERT: K 99 ASP cc_start: 0.9325 (p0) cc_final: 0.9075 (p0) REVERT: K 120 PHE cc_start: 0.9266 (m-80) cc_final: 0.8790 (m-80) REVERT: L 22 ILE cc_start: 0.9724 (mt) cc_final: 0.9439 (mm) REVERT: L 23 ASN cc_start: 0.9563 (m-40) cc_final: 0.9157 (m-40) REVERT: L 26 PHE cc_start: 0.9799 (t80) cc_final: 0.9366 (t80) REVERT: L 30 LYS cc_start: 0.9662 (mmmt) cc_final: 0.9424 (mmmt) REVERT: L 34 HIS cc_start: 0.9530 (t70) cc_final: 0.9168 (t70) REVERT: L 52 MET cc_start: 0.9523 (mtp) cc_final: 0.9016 (mtp) REVERT: L 71 TYR cc_start: 0.9390 (m-80) cc_final: 0.8890 (m-80) REVERT: L 108 MET cc_start: 0.9394 (ttp) cc_final: 0.9000 (mtp) REVERT: L 120 PHE cc_start: 0.9620 (m-80) cc_final: 0.9208 (m-80) REVERT: L 150 LEU cc_start: 0.9872 (tp) cc_final: 0.9663 (tp) REVERT: M 1 MET cc_start: 0.9406 (mmm) cc_final: 0.8175 (tmm) REVERT: M 2 GLN cc_start: 0.9600 (mt0) cc_final: 0.8947 (pp30) REVERT: M 25 TYR cc_start: 0.9549 (m-10) cc_final: 0.9309 (m-80) REVERT: M 26 PHE cc_start: 0.9737 (t80) cc_final: 0.9179 (t80) REVERT: M 27 LEU cc_start: 0.9679 (mt) cc_final: 0.9344 (mt) REVERT: M 35 LYS cc_start: 0.9796 (mttm) cc_final: 0.9551 (mmmm) REVERT: M 52 MET cc_start: 0.9093 (mtm) cc_final: 0.8391 (mtm) REVERT: M 109 ARG cc_start: 0.9706 (ttm-80) cc_final: 0.9261 (tpm170) REVERT: M 155 GLU cc_start: 0.8973 (tp30) cc_final: 0.8188 (pp20) REVERT: M 156 GLN cc_start: 0.7048 (tt0) cc_final: 0.6528 (tt0) REVERT: N 2 GLN cc_start: 0.9476 (mt0) cc_final: 0.9247 (pm20) REVERT: N 26 PHE cc_start: 0.9716 (t80) cc_final: 0.9159 (t80) REVERT: N 27 LEU cc_start: 0.9649 (mt) cc_final: 0.9252 (mt) REVERT: N 30 LYS cc_start: 0.9703 (mmmt) cc_final: 0.9475 (mmtm) REVERT: N 108 MET cc_start: 0.9386 (ptm) cc_final: 0.8875 (ptm) REVERT: N 139 ASP cc_start: 0.9664 (m-30) cc_final: 0.9391 (p0) REVERT: O 8 ILE cc_start: 0.9494 (mm) cc_final: 0.9293 (mm) REVERT: O 26 PHE cc_start: 0.9700 (t80) cc_final: 0.9467 (t80) REVERT: O 32 GLN cc_start: 0.9298 (pt0) cc_final: 0.9055 (pt0) REVERT: O 39 LYS cc_start: 0.9562 (mppt) cc_final: 0.9336 (mmtm) REVERT: O 120 PHE cc_start: 0.9282 (m-10) cc_final: 0.9043 (m-80) REVERT: P 25 TYR cc_start: 0.9661 (m-10) cc_final: 0.9445 (m-80) REVERT: P 26 PHE cc_start: 0.9754 (t80) cc_final: 0.9292 (t80) REVERT: P 32 GLN cc_start: 0.9515 (pm20) cc_final: 0.9244 (pm20) REVERT: P 35 LYS cc_start: 0.9763 (mttm) cc_final: 0.9541 (mtpt) REVERT: P 39 LYS cc_start: 0.9702 (mtmt) cc_final: 0.9500 (mtmm) REVERT: P 120 PHE cc_start: 0.9526 (m-10) cc_final: 0.9241 (m-10) REVERT: P 139 ASP cc_start: 0.9646 (m-30) cc_final: 0.9146 (p0) REVERT: Q 26 PHE cc_start: 0.9784 (t80) cc_final: 0.9390 (t80) REVERT: Q 120 PHE cc_start: 0.9441 (m-10) cc_final: 0.8886 (m-80) REVERT: Q 139 ASP cc_start: 0.9672 (m-30) cc_final: 0.9278 (p0) REVERT: Q 140 LEU cc_start: 0.9810 (mt) cc_final: 0.9480 (mt) REVERT: Q 150 LEU cc_start: 0.9873 (tp) cc_final: 0.9628 (tp) REVERT: R 2 GLN cc_start: 0.9545 (mt0) cc_final: 0.9311 (pm20) REVERT: R 120 PHE cc_start: 0.9586 (m-10) cc_final: 0.9312 (m-80) REVERT: R 155 GLU cc_start: 0.9102 (tp30) cc_final: 0.8756 (tp30) REVERT: S 26 PHE cc_start: 0.9761 (t80) cc_final: 0.9360 (t80) REVERT: S 53 ARG cc_start: 0.9477 (tmm-80) cc_final: 0.9265 (ttp80) REVERT: S 108 MET cc_start: 0.9583 (ptt) cc_final: 0.9301 (ppp) REVERT: S 111 LYS cc_start: 0.9527 (mmmt) cc_final: 0.9320 (mmmt) REVERT: S 120 PHE cc_start: 0.9431 (m-10) cc_final: 0.9155 (m-80) REVERT: T 2 GLN cc_start: 0.9475 (mt0) cc_final: 0.9093 (mm-40) REVERT: T 9 GLU cc_start: 0.9729 (tp30) cc_final: 0.9510 (tp30) REVERT: T 26 PHE cc_start: 0.9736 (t80) cc_final: 0.9334 (t80) REVERT: T 32 GLN cc_start: 0.9406 (pt0) cc_final: 0.9119 (pt0) REVERT: T 52 MET cc_start: 0.9476 (mtt) cc_final: 0.9222 (mtm) REVERT: T 61 ARG cc_start: 0.9835 (tpt170) cc_final: 0.9605 (tpt-90) REVERT: T 108 MET cc_start: 0.9454 (tpt) cc_final: 0.8759 (tpt) REVERT: T 109 ARG cc_start: 0.9536 (ttm-80) cc_final: 0.8940 (tpm170) REVERT: T 116 SER cc_start: 0.9587 (p) cc_final: 0.9080 (p) REVERT: T 120 PHE cc_start: 0.9378 (m-10) cc_final: 0.8936 (m-10) REVERT: T 139 ASP cc_start: 0.9638 (m-30) cc_final: 0.9061 (m-30) REVERT: U 2 GLN cc_start: 0.9581 (mt0) cc_final: 0.9364 (pm20) REVERT: U 26 PHE cc_start: 0.9751 (t80) cc_final: 0.9204 (t80) REVERT: U 34 HIS cc_start: 0.9431 (t70) cc_final: 0.9021 (t70) REVERT: U 35 LYS cc_start: 0.9751 (mttm) cc_final: 0.9535 (mmmm) REVERT: U 91 ARG cc_start: 0.8598 (ttt-90) cc_final: 0.8313 (tpt170) REVERT: U 100 ARG cc_start: 0.9588 (ttm110) cc_final: 0.9320 (ptm160) REVERT: U 101 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9232 (mt) REVERT: U 108 MET cc_start: 0.9460 (ptm) cc_final: 0.9085 (ptm) REVERT: U 120 PHE cc_start: 0.9523 (m-10) cc_final: 0.8976 (m-80) REVERT: U 131 ILE cc_start: 0.9076 (tt) cc_final: 0.8828 (tp) REVERT: V 26 PHE cc_start: 0.9825 (t80) cc_final: 0.9364 (t80) REVERT: V 71 TYR cc_start: 0.8783 (m-80) cc_final: 0.7941 (m-80) REVERT: V 108 MET cc_start: 0.9517 (ptm) cc_final: 0.9029 (ptt) REVERT: V 111 LYS cc_start: 0.9566 (mmmt) cc_final: 0.9361 (mmmt) REVERT: V 120 PHE cc_start: 0.9544 (m-10) cc_final: 0.9206 (m-80) REVERT: V 150 LEU cc_start: 0.9838 (tp) cc_final: 0.9621 (tp) REVERT: W 2 GLN cc_start: 0.9564 (mt0) cc_final: 0.9304 (pm20) REVERT: W 23 ASN cc_start: 0.9660 (m-40) cc_final: 0.9362 (t0) REVERT: W 26 PHE cc_start: 0.9696 (t80) cc_final: 0.9087 (t80) REVERT: W 30 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9360 (mmtt) REVERT: W 56 GLU cc_start: 0.9517 (tt0) cc_final: 0.9135 (tp30) REVERT: W 60 ASP cc_start: 0.9598 (m-30) cc_final: 0.8992 (m-30) REVERT: W 111 LYS cc_start: 0.9574 (mmmt) cc_final: 0.9351 (mmmt) REVERT: X 22 ILE cc_start: 0.9871 (mt) cc_final: 0.9655 (mm) REVERT: X 23 ASN cc_start: 0.9725 (m-40) cc_final: 0.9475 (m-40) REVERT: X 26 PHE cc_start: 0.9793 (t80) cc_final: 0.9290 (t80) REVERT: X 34 HIS cc_start: 0.9735 (t70) cc_final: 0.9509 (t70) REVERT: X 35 LYS cc_start: 0.9819 (mttm) cc_final: 0.9579 (mmmm) REVERT: X 120 PHE cc_start: 0.9609 (m-10) cc_final: 0.9291 (m-80) outliers start: 18 outliers final: 3 residues processed: 1672 average time/residue: 0.5028 time to fit residues: 1238.7168 Evaluate side-chains 1255 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1251 time to evaluate : 3.763 ------------------------------------------------------------------------------- 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: 1.9990 chunk 272 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 282 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 210 optimal weight: 10.0000 chunk 326 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 28 HIS A 34 HIS A 130 HIS C 28 HIS ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS F 76 HIS F 130 HIS ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 HIS E 118 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS G 32 GLN G 76 HIS ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 HIS H 76 HIS ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 HIS J 32 GLN J 76 HIS J 130 HIS K 32 GLN K 76 HIS L 28 HIS L 130 HIS N 76 HIS ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 130 HIS P 14 GLN P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 ASN P 130 HIS Q 28 HIS ** Q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 GLN R 130 HIS S 28 HIS ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 129 HIS U 76 HIS ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 HIS V 34 HIS ** V 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 28 HIS W 130 HIS X 28 HIS ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 130 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32072 Z= 0.191 Angle : 0.661 11.648 43500 Z= 0.327 Chirality : 0.037 0.235 4829 Planarity : 0.003 0.038 5615 Dihedral : 8.450 88.174 4222 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.72 % Allowed : 5.48 % Favored : 93.80 % 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: -1.67 (0.12), residues: 3742 helix: -0.58 (0.08), residues: 2986 sheet: None (None), residues: 0 loop : -2.74 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 37 HIS 0.011 0.001 HIS A 130 PHE 0.033 0.002 PHE M 120 TYR 0.012 0.001 TYR R 25 ARG 0.007 0.001 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1711 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1687 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8996 (mpp) cc_final: 0.8306 (tmm) REVERT: A 2 GLN cc_start: 0.9545 (mt0) cc_final: 0.9276 (pm20) REVERT: A 26 PHE cc_start: 0.9682 (t80) cc_final: 0.9065 (t80) REVERT: A 35 LYS cc_start: 0.9717 (mmmm) cc_final: 0.9469 (mmmm) REVERT: A 56 GLU cc_start: 0.9645 (tm-30) cc_final: 0.9437 (tp30) REVERT: A 71 TYR cc_start: 0.9170 (m-80) cc_final: 0.8586 (m-80) REVERT: A 78 ARG cc_start: 0.9382 (mtm-85) cc_final: 0.9110 (mtm-85) REVERT: A 102 ARG cc_start: 0.8321 (mtt180) cc_final: 0.7657 (mtt180) REVERT: A 120 PHE cc_start: 0.9558 (m-10) cc_final: 0.8977 (m-10) REVERT: A 123 ILE cc_start: 0.8725 (tt) cc_final: 0.8363 (tt) REVERT: B 1 MET cc_start: 0.9240 (mpp) cc_final: 0.8100 (tmm) REVERT: B 2 GLN cc_start: 0.9536 (mt0) cc_final: 0.9072 (tp-100) REVERT: B 10 PHE cc_start: 0.9526 (m-80) cc_final: 0.9246 (m-80) REVERT: B 23 ASN cc_start: 0.9712 (m-40) cc_final: 0.9492 (m-40) REVERT: B 26 PHE cc_start: 0.9610 (t80) cc_final: 0.9099 (t80) REVERT: B 27 LEU cc_start: 0.9333 (mt) cc_final: 0.8599 (mt) REVERT: B 56 GLU cc_start: 0.9455 (tt0) cc_final: 0.9166 (tp30) REVERT: B 78 ARG cc_start: 0.9153 (mtm-85) cc_final: 0.8876 (mtm-85) REVERT: B 111 LYS cc_start: 0.9369 (mmmt) cc_final: 0.9097 (mmmt) REVERT: B 154 ILE cc_start: 0.9580 (pt) cc_final: 0.9335 (mm) REVERT: C 26 PHE cc_start: 0.9737 (t80) cc_final: 0.9501 (t80) REVERT: C 27 LEU cc_start: 0.9467 (mt) cc_final: 0.9136 (mt) REVERT: C 100 ARG cc_start: 0.9566 (ttm110) cc_final: 0.9319 (ptm-80) REVERT: C 102 ARG cc_start: 0.8529 (mtt180) cc_final: 0.8185 (mtp85) REVERT: C 108 MET cc_start: 0.9678 (mtp) cc_final: 0.9410 (mtp) REVERT: C 111 LYS cc_start: 0.9242 (mmpt) cc_final: 0.8996 (mmmt) REVERT: C 120 PHE cc_start: 0.9354 (m-80) cc_final: 0.8432 (m-80) REVERT: C 129 HIS cc_start: 0.9524 (m90) cc_final: 0.9312 (m90) REVERT: D 1 MET cc_start: 0.9199 (mmp) cc_final: 0.8319 (tmm) REVERT: D 2 GLN cc_start: 0.9550 (mt0) cc_final: 0.9161 (pm20) REVERT: D 10 PHE cc_start: 0.9639 (m-80) cc_final: 0.9357 (m-80) REVERT: D 23 ASN cc_start: 0.9504 (m-40) cc_final: 0.9102 (m-40) REVERT: D 26 PHE cc_start: 0.9669 (t80) cc_final: 0.9341 (t80) REVERT: D 27 LEU cc_start: 0.9382 (mt) cc_final: 0.8722 (mt) REVERT: D 52 MET cc_start: 0.9118 (mtp) cc_final: 0.8816 (mtm) REVERT: D 58 LEU cc_start: 0.9302 (mt) cc_final: 0.9060 (mt) REVERT: D 71 TYR cc_start: 0.9570 (m-10) cc_final: 0.9087 (m-80) REVERT: D 111 LYS cc_start: 0.9481 (mmmt) cc_final: 0.9253 (mmmt) REVERT: D 139 ASP cc_start: 0.9454 (m-30) cc_final: 0.9254 (m-30) REVERT: F 6 GLU cc_start: 0.9569 (tp30) cc_final: 0.9321 (tp30) REVERT: F 9 GLU cc_start: 0.9673 (tp30) cc_final: 0.9445 (tp30) REVERT: F 26 PHE cc_start: 0.9728 (t80) cc_final: 0.9171 (t80) REVERT: F 30 LYS cc_start: 0.9544 (mmpt) cc_final: 0.9234 (mmmt) REVERT: F 33 ASP cc_start: 0.9324 (p0) cc_final: 0.9119 (p0) REVERT: F 56 GLU cc_start: 0.9628 (tt0) cc_final: 0.9367 (pp20) REVERT: F 71 TYR cc_start: 0.9536 (m-10) cc_final: 0.9007 (m-80) REVERT: F 98 ILE cc_start: 0.9378 (tt) cc_final: 0.9068 (mm) REVERT: F 102 ARG cc_start: 0.8551 (mtt180) cc_final: 0.7830 (mtt180) REVERT: F 108 MET cc_start: 0.9423 (ptt) cc_final: 0.8925 (ppp) REVERT: F 111 LYS cc_start: 0.9367 (mmmt) cc_final: 0.9046 (mmmt) REVERT: F 130 HIS cc_start: 0.9724 (OUTLIER) cc_final: 0.9418 (t-90) REVERT: E 26 PHE cc_start: 0.9640 (t80) cc_final: 0.9108 (t80) REVERT: E 56 GLU cc_start: 0.9584 (tt0) cc_final: 0.9332 (tp30) REVERT: E 102 ARG cc_start: 0.8346 (mtt180) cc_final: 0.8059 (mtp85) REVERT: E 109 ARG cc_start: 0.9391 (mmt180) cc_final: 0.9144 (mtt-85) REVERT: E 111 LYS cc_start: 0.9372 (mmmt) cc_final: 0.9059 (mmmt) REVERT: E 120 PHE cc_start: 0.9355 (m-10) cc_final: 0.9101 (m-80) REVERT: G 1 MET cc_start: 0.9202 (mpp) cc_final: 0.8835 (mpp) REVERT: G 2 GLN cc_start: 0.9549 (mt0) cc_final: 0.9221 (pm20) REVERT: G 23 ASN cc_start: 0.9712 (m-40) cc_final: 0.9290 (t0) REVERT: G 26 PHE cc_start: 0.9469 (t80) cc_final: 0.9227 (t80) REVERT: G 27 LEU cc_start: 0.9407 (mt) cc_final: 0.8801 (mt) REVERT: G 35 LYS cc_start: 0.9823 (mmmm) cc_final: 0.9491 (mmmm) REVERT: G 71 TYR cc_start: 0.9498 (m-80) cc_final: 0.9186 (m-80) REVERT: G 78 ARG cc_start: 0.9303 (mtm-85) cc_final: 0.9014 (mtm-85) REVERT: G 102 ARG cc_start: 0.8265 (mtt180) cc_final: 0.7960 (mtp85) REVERT: G 111 LYS cc_start: 0.9328 (mmpt) cc_final: 0.9120 (mmmt) REVERT: G 139 ASP cc_start: 0.9340 (m-30) cc_final: 0.9072 (m-30) REVERT: G 154 ILE cc_start: 0.9507 (pt) cc_final: 0.9254 (mt) REVERT: H 1 MET cc_start: 0.9537 (mpp) cc_final: 0.9197 (mpp) REVERT: H 26 PHE cc_start: 0.9659 (t80) cc_final: 0.9278 (t80) REVERT: H 27 LEU cc_start: 0.9350 (mt) cc_final: 0.8902 (mt) REVERT: H 35 LYS cc_start: 0.9850 (mmmm) cc_final: 0.9556 (mmmm) REVERT: H 52 MET cc_start: 0.8733 (mtt) cc_final: 0.8433 (mtt) REVERT: H 78 ARG cc_start: 0.9374 (mtm-85) cc_final: 0.8943 (mtm-85) REVERT: H 111 LYS cc_start: 0.9331 (mmmt) cc_final: 0.9040 (mmmt) REVERT: H 116 SER cc_start: 0.9667 (m) cc_final: 0.9091 (p) REVERT: H 120 PHE cc_start: 0.9432 (m-10) cc_final: 0.9068 (m-80) REVERT: I 2 GLN cc_start: 0.9513 (mt0) cc_final: 0.9138 (mm-40) REVERT: I 6 GLU cc_start: 0.9484 (tp30) cc_final: 0.9269 (tp30) REVERT: I 19 LEU cc_start: 0.9784 (mp) cc_final: 0.9571 (mt) REVERT: I 23 ASN cc_start: 0.9734 (m-40) cc_final: 0.9452 (t0) REVERT: I 24 GLN cc_start: 0.9459 (tt0) cc_final: 0.9252 (tm-30) REVERT: I 26 PHE cc_start: 0.9687 (t80) cc_final: 0.9330 (t80) REVERT: I 35 LYS cc_start: 0.9811 (mmmm) cc_final: 0.9485 (mmmm) REVERT: I 78 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8857 (mtm-85) REVERT: I 120 PHE cc_start: 0.9404 (m-80) cc_final: 0.8697 (m-80) REVERT: I 131 ILE cc_start: 0.9141 (tt) cc_final: 0.8838 (tt) REVERT: J 2 GLN cc_start: 0.9555 (mt0) cc_final: 0.9024 (mm-40) REVERT: J 26 PHE cc_start: 0.9660 (t80) cc_final: 0.9291 (t80) REVERT: J 35 LYS cc_start: 0.9804 (mmmm) cc_final: 0.9535 (mmmm) REVERT: J 91 ARG cc_start: 0.8750 (ttt90) cc_final: 0.8382 (tpt170) REVERT: J 111 LYS cc_start: 0.9580 (mmpt) cc_final: 0.9350 (mmmt) REVERT: J 130 HIS cc_start: 0.9670 (t-90) cc_final: 0.9463 (t-90) REVERT: J 131 ILE cc_start: 0.9257 (tt) cc_final: 0.8938 (tt) REVERT: J 134 LEU cc_start: 0.9768 (mp) cc_final: 0.9543 (pp) REVERT: J 156 GLN cc_start: 0.6317 (pt0) cc_final: 0.6013 (pt0) REVERT: K 1 MET cc_start: 0.9251 (mpp) cc_final: 0.8340 (tmm) REVERT: K 2 GLN cc_start: 0.9551 (mt0) cc_final: 0.9116 (pp30) REVERT: K 26 PHE cc_start: 0.9653 (t80) cc_final: 0.9179 (t80) REVERT: K 60 ASP cc_start: 0.9814 (p0) cc_final: 0.9580 (p0) REVERT: K 78 ARG cc_start: 0.9362 (mtm-85) cc_final: 0.9151 (mtm-85) REVERT: K 109 ARG cc_start: 0.9575 (mtt-85) cc_final: 0.9210 (mtt-85) REVERT: K 111 LYS cc_start: 0.9334 (mmpt) cc_final: 0.9065 (mmmt) REVERT: K 120 PHE cc_start: 0.9302 (m-80) cc_final: 0.8842 (m-80) REVERT: K 139 ASP cc_start: 0.9313 (m-30) cc_final: 0.9055 (m-30) REVERT: L 23 ASN cc_start: 0.9646 (m-40) cc_final: 0.9331 (m-40) REVERT: L 26 PHE cc_start: 0.9730 (t80) cc_final: 0.9125 (t80) REVERT: L 27 LEU cc_start: 0.9430 (mt) cc_final: 0.8733 (mt) REVERT: L 34 HIS cc_start: 0.9362 (t70) cc_final: 0.9031 (t-90) REVERT: L 50 ASP cc_start: 0.9865 (m-30) cc_final: 0.9656 (m-30) REVERT: L 52 MET cc_start: 0.9440 (mtp) cc_final: 0.8799 (mtp) REVERT: L 53 ARG cc_start: 0.9212 (ttp-110) cc_final: 0.8924 (ptp-110) REVERT: L 102 ARG cc_start: 0.8424 (mtt180) cc_final: 0.7820 (mtp85) REVERT: L 109 ARG cc_start: 0.9528 (mtp85) cc_final: 0.9014 (mtm110) REVERT: L 120 PHE cc_start: 0.9518 (m-80) cc_final: 0.9109 (m-80) REVERT: L 156 GLN cc_start: 0.5899 (pt0) cc_final: 0.5243 (pt0) REVERT: M 1 MET cc_start: 0.9219 (mmm) cc_final: 0.8207 (tmm) REVERT: M 2 GLN cc_start: 0.9598 (mt0) cc_final: 0.9017 (pp30) REVERT: M 52 MET cc_start: 0.8391 (mtm) cc_final: 0.8190 (mtm) REVERT: M 111 LYS cc_start: 0.9374 (mmpt) cc_final: 0.9146 (mmmt) REVERT: M 116 SER cc_start: 0.9746 (m) cc_final: 0.9483 (p) REVERT: M 120 PHE cc_start: 0.9522 (m-80) cc_final: 0.9094 (m-10) REVERT: M 123 ILE cc_start: 0.9149 (tt) cc_final: 0.8892 (tt) REVERT: M 156 GLN cc_start: 0.7971 (tt0) cc_final: 0.7290 (tt0) REVERT: N 2 GLN cc_start: 0.9565 (mt0) cc_final: 0.8969 (pp30) REVERT: N 10 PHE cc_start: 0.9614 (m-80) cc_final: 0.9299 (m-80) REVERT: N 23 ASN cc_start: 0.9508 (m-40) cc_final: 0.9212 (m-40) REVERT: N 26 PHE cc_start: 0.9586 (t80) cc_final: 0.9327 (t80) REVERT: N 31 LEU cc_start: 0.9711 (mt) cc_final: 0.9337 (mt) REVERT: N 102 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7850 (mtp85) REVERT: N 111 LYS cc_start: 0.9217 (mmpt) cc_final: 0.8989 (mmmt) REVERT: N 139 ASP cc_start: 0.9411 (m-30) cc_final: 0.9161 (m-30) REVERT: O 26 PHE cc_start: 0.9664 (t80) cc_final: 0.9230 (t80) REVERT: O 32 GLN cc_start: 0.8936 (pt0) cc_final: 0.8666 (pt0) REVERT: O 91 ARG cc_start: 0.8699 (ttt90) cc_final: 0.8416 (tpt170) REVERT: O 120 PHE cc_start: 0.9186 (m-10) cc_final: 0.8909 (m-80) REVERT: O 130 HIS cc_start: 0.9767 (t-90) cc_final: 0.9558 (t-90) REVERT: O 131 ILE cc_start: 0.9286 (tt) cc_final: 0.9013 (tt) REVERT: O 156 GLN cc_start: 0.6749 (pp30) cc_final: 0.6534 (pp30) REVERT: P 23 ASN cc_start: 0.9848 (m-40) cc_final: 0.9417 (t0) REVERT: P 26 PHE cc_start: 0.9582 (t80) cc_final: 0.8981 (t80) REVERT: P 27 LEU cc_start: 0.9347 (mt) cc_final: 0.8818 (mt) REVERT: P 32 GLN cc_start: 0.9204 (pm20) cc_final: 0.8801 (pm20) REVERT: P 43 TYR cc_start: 0.9642 (t80) cc_final: 0.9362 (t80) REVERT: P 61 ARG cc_start: 0.9758 (tpt-90) cc_final: 0.9524 (tpt170) REVERT: P 102 ARG cc_start: 0.8275 (mtt180) cc_final: 0.7947 (mtp85) REVERT: P 108 MET cc_start: 0.9505 (ptt) cc_final: 0.9056 (ppp) REVERT: P 111 LYS cc_start: 0.9288 (mmpt) cc_final: 0.9084 (mmmt) REVERT: P 120 PHE cc_start: 0.9493 (m-10) cc_final: 0.9219 (m-10) REVERT: Q 10 PHE cc_start: 0.9508 (m-80) cc_final: 0.9237 (m-80) REVERT: Q 26 PHE cc_start: 0.9665 (t80) cc_final: 0.9255 (t80) REVERT: Q 35 LYS cc_start: 0.9734 (mmmm) cc_final: 0.9498 (mmmm) REVERT: Q 56 GLU cc_start: 0.9603 (tm-30) cc_final: 0.9382 (tp30) REVERT: Q 78 ARG cc_start: 0.9365 (mtm-85) cc_final: 0.9131 (mtm-85) REVERT: Q 102 ARG cc_start: 0.8205 (mtt180) cc_final: 0.7815 (mtp85) REVERT: Q 120 PHE cc_start: 0.9432 (m-10) cc_final: 0.9180 (m-80) REVERT: Q 139 ASP cc_start: 0.9383 (m-30) cc_final: 0.9165 (m-30) REVERT: R 2 GLN cc_start: 0.9508 (mt0) cc_final: 0.9091 (pp30) REVERT: R 23 ASN cc_start: 0.9670 (m-40) cc_final: 0.9074 (p0) REVERT: R 24 GLN cc_start: 0.9481 (tt0) cc_final: 0.9071 (tt0) REVERT: R 35 LYS cc_start: 0.9743 (mtpp) cc_final: 0.9528 (mtpt) REVERT: R 52 MET cc_start: 0.9412 (mtm) cc_final: 0.9065 (mtm) REVERT: R 56 GLU cc_start: 0.9445 (tt0) cc_final: 0.9121 (tp30) REVERT: R 102 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7920 (mtp85) REVERT: R 105 ILE cc_start: 0.9653 (mt) cc_final: 0.9451 (tp) REVERT: R 108 MET cc_start: 0.9403 (ptt) cc_final: 0.9086 (ppp) REVERT: R 109 ARG cc_start: 0.9408 (mmt180) cc_final: 0.8919 (mtp180) REVERT: R 111 LYS cc_start: 0.9367 (mmpt) cc_final: 0.9127 (mmmt) REVERT: R 155 GLU cc_start: 0.9039 (tp30) cc_final: 0.8800 (tp30) REVERT: S 23 ASN cc_start: 0.9780 (m-40) cc_final: 0.9574 (t0) REVERT: S 26 PHE cc_start: 0.9679 (t80) cc_final: 0.9181 (t80) REVERT: S 27 LEU cc_start: 0.9361 (mt) cc_final: 0.8802 (mt) REVERT: S 100 ARG cc_start: 0.9103 (mmt180) cc_final: 0.8788 (mmm160) REVERT: S 102 ARG cc_start: 0.8269 (mtt180) cc_final: 0.7917 (mtp85) REVERT: S 108 MET cc_start: 0.9414 (ptt) cc_final: 0.8869 (ppp) REVERT: S 109 ARG cc_start: 0.9442 (mtt-85) cc_final: 0.8851 (tpm170) REVERT: S 111 LYS cc_start: 0.9284 (mmmt) cc_final: 0.9041 (mmmt) REVERT: S 139 ASP cc_start: 0.9379 (m-30) cc_final: 0.9087 (m-30) REVERT: T 1 MET cc_start: 0.9442 (mpp) cc_final: 0.8253 (tmm) REVERT: T 2 GLN cc_start: 0.9509 (mt0) cc_final: 0.9150 (mm-40) REVERT: T 6 GLU cc_start: 0.9530 (tp30) cc_final: 0.9295 (tp30) REVERT: T 26 PHE cc_start: 0.9689 (t80) cc_final: 0.9409 (t80) REVERT: T 32 GLN cc_start: 0.9144 (pt0) cc_final: 0.8749 (pt0) REVERT: T 108 MET cc_start: 0.9348 (tpt) cc_final: 0.8868 (tpt) REVERT: T 111 LYS cc_start: 0.9340 (mmpt) cc_final: 0.9098 (mmmt) REVERT: T 116 SER cc_start: 0.9401 (p) cc_final: 0.8907 (p) REVERT: T 120 PHE cc_start: 0.9494 (m-10) cc_final: 0.9178 (m-80) REVERT: T 139 ASP cc_start: 0.9322 (m-30) cc_final: 0.8960 (m-30) REVERT: U 10 PHE cc_start: 0.9521 (m-80) cc_final: 0.9228 (m-80) REVERT: U 26 PHE cc_start: 0.9637 (t80) cc_final: 0.9009 (t80) REVERT: U 27 LEU cc_start: 0.9556 (tp) cc_final: 0.8980 (mt) REVERT: U 34 HIS cc_start: 0.9411 (t70) cc_final: 0.9072 (t70) REVERT: U 78 ARG cc_start: 0.9209 (mtm-85) cc_final: 0.8868 (mtm-85) REVERT: U 102 ARG cc_start: 0.8412 (mtt180) cc_final: 0.8060 (mtp85) REVERT: U 108 MET cc_start: 0.9537 (ptm) cc_final: 0.9072 (ptm) REVERT: V 23 ASN cc_start: 0.9657 (m110) cc_final: 0.9370 (t0) REVERT: V 26 PHE cc_start: 0.9747 (t80) cc_final: 0.9186 (t80) REVERT: V 27 LEU cc_start: 0.9461 (mt) cc_final: 0.8806 (mt) REVERT: V 30 LYS cc_start: 0.9528 (mmpt) cc_final: 0.9290 (mmmt) REVERT: V 102 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7954 (mtp85) REVERT: V 108 MET cc_start: 0.9620 (ptm) cc_final: 0.9257 (ptm) REVERT: V 111 LYS cc_start: 0.9360 (mmmt) cc_final: 0.9052 (mmmt) REVERT: V 153 VAL cc_start: 0.9661 (m) cc_final: 0.9119 (p) REVERT: W 2 GLN cc_start: 0.9558 (mt0) cc_final: 0.9206 (pm20) REVERT: W 10 PHE cc_start: 0.9511 (m-80) cc_final: 0.9258 (m-80) REVERT: W 23 ASN cc_start: 0.9718 (m-40) cc_final: 0.9421 (t0) REVERT: W 26 PHE cc_start: 0.9509 (t80) cc_final: 0.9105 (t80) REVERT: W 32 GLN cc_start: 0.9026 (pt0) cc_final: 0.8619 (pt0) REVERT: W 56 GLU cc_start: 0.9496 (tt0) cc_final: 0.9023 (tp30) REVERT: W 60 ASP cc_start: 0.9551 (m-30) cc_final: 0.9181 (m-30) REVERT: W 91 ARG cc_start: 0.8801 (ttt90) cc_final: 0.8544 (tpt170) REVERT: W 100 ARG cc_start: 0.9367 (mmm160) cc_final: 0.8968 (mmm-85) REVERT: W 102 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7385 (mtt180) REVERT: W 105 ILE cc_start: 0.9656 (mt) cc_final: 0.9407 (mp) REVERT: W 108 MET cc_start: 0.9268 (ptt) cc_final: 0.8859 (ppp) REVERT: W 111 LYS cc_start: 0.9291 (mmmt) cc_final: 0.8905 (mmmt) REVERT: W 120 PHE cc_start: 0.9265 (m-80) cc_final: 0.8786 (m-80) REVERT: W 130 HIS cc_start: 0.9709 (OUTLIER) cc_final: 0.9365 (t-90) REVERT: W 155 GLU cc_start: 0.9070 (tp30) cc_final: 0.8356 (tm-30) REVERT: X 23 ASN cc_start: 0.9800 (m-40) cc_final: 0.9563 (t0) REVERT: X 26 PHE cc_start: 0.9758 (t80) cc_final: 0.9261 (t80) REVERT: X 27 LEU cc_start: 0.9428 (mt) cc_final: 0.8726 (mt) REVERT: X 102 ARG cc_start: 0.8364 (mtt180) cc_final: 0.8062 (mtp85) REVERT: X 108 MET cc_start: 0.9679 (ptp) cc_final: 0.9395 (ppp) REVERT: X 111 LYS cc_start: 0.9369 (mmpt) cc_final: 0.9138 (mmmt) REVERT: X 130 HIS cc_start: 0.9715 (OUTLIER) cc_final: 0.9197 (t-90) outliers start: 24 outliers final: 5 residues processed: 1698 average time/residue: 0.5088 time to fit residues: 1274.3272 Evaluate side-chains 1300 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1292 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 327 optimal weight: 9.9990 chunk 353 optimal weight: 6.9990 chunk 291 optimal weight: 0.9980 chunk 324 optimal weight: 5.9990 chunk 111 optimal weight: 0.0030 chunk 262 optimal weight: 8.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 76 HIS A 156 GLN B 76 HIS B 112 HIS B 129 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS C 130 HIS ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS E 34 HIS E 76 HIS E 129 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 HIS ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS H 112 HIS H 129 HIS I 76 HIS ** J 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 HIS L 130 HIS M 129 HIS ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS O 76 HIS P 130 HIS Q 34 HIS Q 76 HIS Q 130 HIS Q 156 GLN R 76 HIS ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 HIS S 76 HIS S 112 HIS S 129 HIS S 156 GLN ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 130 HIS T 156 GLN U 70 ASN V 23 ASN V 34 HIS V 76 HIS V 112 HIS V 156 GLN W 24 GLN W 34 HIS W 112 HIS ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 GLN X 76 HIS X 129 HIS X 156 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32072 Z= 0.213 Angle : 0.670 18.350 43500 Z= 0.329 Chirality : 0.037 0.204 4829 Planarity : 0.003 0.035 5615 Dihedral : 8.191 88.978 4222 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.30 % Allowed : 5.33 % Favored : 94.37 % 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: -0.77 (0.13), residues: 3742 helix: 0.10 (0.09), residues: 3018 sheet: None (None), residues: 0 loop : -2.82 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 37 HIS 0.013 0.001 HIS A 129 PHE 0.028 0.002 PHE J 120 TYR 0.024 0.001 TYR U 25 ARG 0.008 0.001 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1561 time to evaluate : 3.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9250 (mpp) cc_final: 0.8355 (tmm) REVERT: A 23 ASN cc_start: 0.9821 (m-40) cc_final: 0.9596 (m-40) REVERT: A 26 PHE cc_start: 0.9671 (t80) cc_final: 0.9137 (t80) REVERT: A 78 ARG cc_start: 0.9432 (mtm-85) cc_final: 0.9141 (mtm-85) REVERT: A 102 ARG cc_start: 0.8227 (mtt180) cc_final: 0.7687 (mtt180) REVERT: A 108 MET cc_start: 0.9278 (mmt) cc_final: 0.9061 (mmt) REVERT: A 111 LYS cc_start: 0.9212 (mmpt) cc_final: 0.8904 (mmmt) REVERT: A 120 PHE cc_start: 0.9622 (m-10) cc_final: 0.9286 (m-10) REVERT: A 139 ASP cc_start: 0.9398 (m-30) cc_final: 0.9166 (m-30) REVERT: B 1 MET cc_start: 0.9339 (mpp) cc_final: 0.8490 (tmm) REVERT: B 2 GLN cc_start: 0.9513 (mt0) cc_final: 0.9074 (tp-100) REVERT: B 26 PHE cc_start: 0.9538 (t80) cc_final: 0.9100 (t80) REVERT: B 27 LEU cc_start: 0.9170 (mt) cc_final: 0.8917 (mm) REVERT: B 34 HIS cc_start: 0.9314 (t-90) cc_final: 0.9104 (t-90) REVERT: B 35 LYS cc_start: 0.9762 (mtpp) cc_final: 0.9500 (mmmm) REVERT: B 50 ASP cc_start: 0.9802 (t70) cc_final: 0.9544 (t0) REVERT: B 56 GLU cc_start: 0.9493 (tt0) cc_final: 0.9216 (tp30) REVERT: B 73 ARG cc_start: 0.9076 (mtm110) cc_final: 0.8650 (mpp80) REVERT: B 100 ARG cc_start: 0.9473 (mmt180) cc_final: 0.9243 (mmm160) REVERT: B 111 LYS cc_start: 0.9158 (mmmt) cc_final: 0.8839 (mmmt) REVERT: B 120 PHE cc_start: 0.9480 (m-80) cc_final: 0.9128 (m-80) REVERT: B 139 ASP cc_start: 0.9514 (m-30) cc_final: 0.9309 (m-30) REVERT: B 154 ILE cc_start: 0.9633 (pt) cc_final: 0.9342 (mm) REVERT: C 26 PHE cc_start: 0.9717 (t80) cc_final: 0.9350 (t80) REVERT: C 27 LEU cc_start: 0.9468 (mt) cc_final: 0.8999 (mt) REVERT: C 102 ARG cc_start: 0.8501 (mtt180) cc_final: 0.8164 (mtp85) REVERT: C 108 MET cc_start: 0.9687 (mtp) cc_final: 0.9468 (mtp) REVERT: C 111 LYS cc_start: 0.9204 (mmpt) cc_final: 0.8905 (mmmt) REVERT: C 120 PHE cc_start: 0.9281 (m-80) cc_final: 0.8567 (m-80) REVERT: C 123 ILE cc_start: 0.9571 (tt) cc_final: 0.9289 (tt) REVERT: C 130 HIS cc_start: 0.8894 (t-90) cc_final: 0.8509 (t-90) REVERT: C 131 ILE cc_start: 0.8417 (tp) cc_final: 0.8200 (tp) REVERT: C 156 GLN cc_start: 0.6227 (tt0) cc_final: 0.5754 (tt0) REVERT: D 1 MET cc_start: 0.9183 (mmp) cc_final: 0.8341 (tmm) REVERT: D 2 GLN cc_start: 0.9577 (mt0) cc_final: 0.9265 (pm20) REVERT: D 26 PHE cc_start: 0.9660 (t80) cc_final: 0.9399 (t80) REVERT: D 27 LEU cc_start: 0.9338 (mt) cc_final: 0.8805 (mt) REVERT: D 52 MET cc_start: 0.8992 (mtp) cc_final: 0.8471 (mtm) REVERT: D 139 ASP cc_start: 0.9497 (m-30) cc_final: 0.9265 (m-30) REVERT: F 6 GLU cc_start: 0.9558 (tp30) cc_final: 0.9320 (tp30) REVERT: F 9 GLU cc_start: 0.9660 (tp30) cc_final: 0.9460 (tp30) REVERT: F 26 PHE cc_start: 0.9727 (t80) cc_final: 0.9243 (t80) REVERT: F 56 GLU cc_start: 0.9610 (tt0) cc_final: 0.9390 (tp30) REVERT: F 60 ASP cc_start: 0.9826 (p0) cc_final: 0.9493 (p0) REVERT: F 71 TYR cc_start: 0.9504 (m-10) cc_final: 0.9067 (m-10) REVERT: F 102 ARG cc_start: 0.8490 (mtt180) cc_final: 0.7845 (mtt180) REVERT: F 108 MET cc_start: 0.9333 (ptt) cc_final: 0.8785 (ppp) REVERT: F 109 ARG cc_start: 0.9348 (mtt-85) cc_final: 0.9094 (mtp180) REVERT: F 111 LYS cc_start: 0.9336 (mmmt) cc_final: 0.9018 (mmmt) REVERT: E 26 PHE cc_start: 0.9621 (t80) cc_final: 0.9226 (t80) REVERT: E 60 ASP cc_start: 0.9891 (p0) cc_final: 0.9594 (p0) REVERT: E 102 ARG cc_start: 0.8316 (mtt180) cc_final: 0.8041 (mtp85) REVERT: E 111 LYS cc_start: 0.9406 (mmmt) cc_final: 0.9100 (mmmt) REVERT: E 120 PHE cc_start: 0.9390 (m-10) cc_final: 0.9082 (m-10) REVERT: G 1 MET cc_start: 0.9005 (mpp) cc_final: 0.8776 (mpp) REVERT: G 2 GLN cc_start: 0.9568 (mt0) cc_final: 0.9294 (pm20) REVERT: G 23 ASN cc_start: 0.9702 (m-40) cc_final: 0.9194 (t0) REVERT: G 26 PHE cc_start: 0.9451 (t80) cc_final: 0.9237 (t80) REVERT: G 27 LEU cc_start: 0.9386 (mt) cc_final: 0.8726 (mt) REVERT: G 35 LYS cc_start: 0.9823 (mmmm) cc_final: 0.9536 (mmmm) REVERT: G 102 ARG cc_start: 0.8197 (mtt180) cc_final: 0.7965 (mtp85) REVERT: G 109 ARG cc_start: 0.9362 (mtt-85) cc_final: 0.9135 (ttt180) REVERT: G 139 ASP cc_start: 0.9335 (m-30) cc_final: 0.9060 (m-30) REVERT: G 154 ILE cc_start: 0.9609 (pt) cc_final: 0.9247 (mt) REVERT: H 1 MET cc_start: 0.9474 (mpp) cc_final: 0.9032 (mpp) REVERT: H 26 PHE cc_start: 0.9647 (t80) cc_final: 0.9260 (t80) REVERT: H 27 LEU cc_start: 0.9266 (mt) cc_final: 0.9032 (mt) REVERT: H 35 LYS cc_start: 0.9828 (mmmm) cc_final: 0.9571 (mmmm) REVERT: H 100 ARG cc_start: 0.9304 (mmt180) cc_final: 0.9101 (mmm160) REVERT: H 111 LYS cc_start: 0.9214 (mmmt) cc_final: 0.8918 (mmmt) REVERT: H 116 SER cc_start: 0.9624 (m) cc_final: 0.9392 (p) REVERT: H 120 PHE cc_start: 0.9563 (m-10) cc_final: 0.9230 (m-10) REVERT: I 2 GLN cc_start: 0.9529 (mt0) cc_final: 0.9152 (mm-40) REVERT: I 6 GLU cc_start: 0.9458 (tp30) cc_final: 0.9220 (tp30) REVERT: I 10 PHE cc_start: 0.9547 (m-80) cc_final: 0.8999 (m-80) REVERT: I 23 ASN cc_start: 0.9660 (m-40) cc_final: 0.9229 (t0) REVERT: I 24 GLN cc_start: 0.9514 (tt0) cc_final: 0.9208 (tm-30) REVERT: I 26 PHE cc_start: 0.9667 (t80) cc_final: 0.9253 (t80) REVERT: I 27 LEU cc_start: 0.9405 (mt) cc_final: 0.8837 (mt) REVERT: I 71 TYR cc_start: 0.9587 (m-80) cc_final: 0.9110 (m-80) REVERT: I 111 LYS cc_start: 0.9327 (mmpt) cc_final: 0.9119 (mmmt) REVERT: I 120 PHE cc_start: 0.9389 (m-80) cc_final: 0.8938 (m-10) REVERT: J 1 MET cc_start: 0.9354 (mpp) cc_final: 0.8978 (mpp) REVERT: J 111 LYS cc_start: 0.9444 (mmpt) cc_final: 0.9227 (mmmt) REVERT: J 139 ASP cc_start: 0.9593 (m-30) cc_final: 0.9044 (m-30) REVERT: K 2 GLN cc_start: 0.9552 (mt0) cc_final: 0.9139 (pp30) REVERT: K 26 PHE cc_start: 0.9662 (t80) cc_final: 0.9293 (t80) REVERT: K 120 PHE cc_start: 0.9459 (m-80) cc_final: 0.8870 (m-80) REVERT: K 139 ASP cc_start: 0.9342 (m-30) cc_final: 0.8839 (m-30) REVERT: L 26 PHE cc_start: 0.9699 (t80) cc_final: 0.9418 (t80) REVERT: L 27 LEU cc_start: 0.9470 (mt) cc_final: 0.9112 (mt) REVERT: L 34 HIS cc_start: 0.9288 (t70) cc_final: 0.8966 (t-90) REVERT: L 35 LYS cc_start: 0.9803 (mmtp) cc_final: 0.9598 (mmmm) REVERT: L 52 MET cc_start: 0.9540 (mtp) cc_final: 0.8988 (mtp) REVERT: L 108 MET cc_start: 0.9716 (ptm) cc_final: 0.9173 (ptm) REVERT: L 111 LYS cc_start: 0.9333 (mmpt) cc_final: 0.9047 (mmmt) REVERT: L 120 PHE cc_start: 0.9533 (m-80) cc_final: 0.9069 (m-80) REVERT: L 130 HIS cc_start: 0.8987 (t-90) cc_final: 0.8641 (t-90) REVERT: L 143 LYS cc_start: 0.9254 (tmmt) cc_final: 0.8889 (tmtt) REVERT: M 1 MET cc_start: 0.9276 (mmm) cc_final: 0.8262 (tmm) REVERT: M 2 GLN cc_start: 0.9622 (mt0) cc_final: 0.9009 (pp30) REVERT: M 26 PHE cc_start: 0.9628 (t80) cc_final: 0.9273 (t80) REVERT: M 27 LEU cc_start: 0.9409 (mt) cc_final: 0.8801 (mt) REVERT: M 52 MET cc_start: 0.8908 (mtm) cc_final: 0.8551 (mtm) REVERT: M 100 ARG cc_start: 0.9609 (mmt90) cc_final: 0.9407 (mmm-85) REVERT: M 109 ARG cc_start: 0.9496 (ttm-80) cc_final: 0.9200 (tpm170) REVERT: M 116 SER cc_start: 0.9662 (m) cc_final: 0.9449 (p) REVERT: M 120 PHE cc_start: 0.9629 (m-80) cc_final: 0.9197 (m-10) REVERT: M 123 ILE cc_start: 0.9124 (tt) cc_final: 0.8885 (tt) REVERT: M 139 ASP cc_start: 0.9478 (m-30) cc_final: 0.9256 (m-30) REVERT: M 155 GLU cc_start: 0.9102 (tp30) cc_final: 0.8513 (mp0) REVERT: M 156 GLN cc_start: 0.7774 (tt0) cc_final: 0.6066 (tt0) REVERT: N 2 GLN cc_start: 0.9584 (mt0) cc_final: 0.8995 (pp30) REVERT: N 23 ASN cc_start: 0.9556 (m-40) cc_final: 0.9099 (t0) REVERT: N 26 PHE cc_start: 0.9567 (t80) cc_final: 0.9355 (t80) REVERT: N 27 LEU cc_start: 0.9411 (mt) cc_final: 0.8758 (mt) REVERT: N 86 MET cc_start: 0.9533 (pmm) cc_final: 0.9304 (pmm) REVERT: N 102 ARG cc_start: 0.7966 (mtt180) cc_final: 0.7636 (mtp85) REVERT: N 108 MET cc_start: 0.9149 (ptt) cc_final: 0.8305 (ppp) REVERT: N 109 ARG cc_start: 0.9384 (mtt180) cc_final: 0.8892 (mmm160) REVERT: N 111 LYS cc_start: 0.9133 (mmpt) cc_final: 0.8828 (mmmt) REVERT: N 114 ILE cc_start: 0.8586 (mp) cc_final: 0.8281 (mm) REVERT: N 120 PHE cc_start: 0.9175 (m-80) cc_final: 0.8972 (m-80) REVERT: N 131 ILE cc_start: 0.9212 (tt) cc_final: 0.8834 (tt) REVERT: N 139 ASP cc_start: 0.9412 (m-30) cc_final: 0.9165 (m-30) REVERT: O 26 PHE cc_start: 0.9565 (t80) cc_final: 0.9192 (t80) REVERT: O 32 GLN cc_start: 0.9267 (pt0) cc_final: 0.9001 (pt0) REVERT: O 86 MET cc_start: 0.9856 (ptp) cc_final: 0.9575 (ptp) REVERT: O 102 ARG cc_start: 0.8626 (mtt180) cc_final: 0.7962 (mtp180) REVERT: O 108 MET cc_start: 0.9572 (mpp) cc_final: 0.9351 (mmt) REVERT: O 111 LYS cc_start: 0.9276 (mmpt) cc_final: 0.8971 (mmmt) REVERT: O 120 PHE cc_start: 0.9403 (m-10) cc_final: 0.9183 (m-80) REVERT: O 156 GLN cc_start: 0.7080 (pp30) cc_final: 0.6840 (pp30) REVERT: P 1 MET cc_start: 0.9357 (mpp) cc_final: 0.8611 (tmm) REVERT: P 2 GLN cc_start: 0.9482 (pm20) cc_final: 0.9224 (pm20) REVERT: P 23 ASN cc_start: 0.9835 (m-40) cc_final: 0.9628 (m-40) REVERT: P 26 PHE cc_start: 0.9473 (t80) cc_final: 0.8997 (t80) REVERT: P 27 LEU cc_start: 0.9444 (mt) cc_final: 0.9059 (mt) REVERT: P 102 ARG cc_start: 0.8273 (mtt180) cc_final: 0.8034 (mtp85) REVERT: P 108 MET cc_start: 0.9579 (ptt) cc_final: 0.9168 (ppp) REVERT: P 109 ARG cc_start: 0.9374 (mtp180) cc_final: 0.8771 (tpm170) REVERT: P 111 LYS cc_start: 0.9279 (mmpt) cc_final: 0.9058 (mmmt) REVERT: P 120 PHE cc_start: 0.9610 (m-10) cc_final: 0.9341 (m-10) REVERT: P 139 ASP cc_start: 0.9298 (m-30) cc_final: 0.9067 (m-30) REVERT: Q 26 PHE cc_start: 0.9656 (t80) cc_final: 0.9033 (t80) REVERT: Q 27 LEU cc_start: 0.9387 (mt) cc_final: 0.8872 (mt) REVERT: Q 53 ARG cc_start: 0.9307 (ptp90) cc_final: 0.9084 (ptp-170) REVERT: Q 56 GLU cc_start: 0.9594 (tm-30) cc_final: 0.9375 (tp30) REVERT: Q 59 THR cc_start: 0.9787 (m) cc_final: 0.9587 (m) REVERT: Q 91 ARG cc_start: 0.8549 (ttt-90) cc_final: 0.8319 (tpt170) REVERT: Q 102 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7838 (mtp85) REVERT: Q 120 PHE cc_start: 0.9465 (m-10) cc_final: 0.9232 (m-10) REVERT: Q 131 ILE cc_start: 0.8832 (tt) cc_final: 0.8598 (tt) REVERT: Q 139 ASP cc_start: 0.9340 (m-30) cc_final: 0.8930 (m-30) REVERT: R 2 GLN cc_start: 0.9569 (mt0) cc_final: 0.9180 (pp30) REVERT: R 35 LYS cc_start: 0.9742 (mtpp) cc_final: 0.9526 (mtpt) REVERT: R 52 MET cc_start: 0.9388 (mtm) cc_final: 0.8944 (mtm) REVERT: R 56 GLU cc_start: 0.9433 (tt0) cc_final: 0.9176 (tp30) REVERT: R 108 MET cc_start: 0.9280 (ptt) cc_final: 0.8830 (ppp) REVERT: R 111 LYS cc_start: 0.9323 (mmpt) cc_final: 0.9057 (mmmt) REVERT: S 23 ASN cc_start: 0.9666 (m-40) cc_final: 0.9086 (t0) REVERT: S 26 PHE cc_start: 0.9655 (t80) cc_final: 0.9316 (t80) REVERT: S 27 LEU cc_start: 0.9178 (mt) cc_final: 0.8362 (mt) REVERT: S 56 GLU cc_start: 0.9624 (tt0) cc_final: 0.9268 (tp30) REVERT: S 86 MET cc_start: 0.9754 (ptp) cc_final: 0.9551 (ptp) REVERT: S 102 ARG cc_start: 0.8293 (mtt180) cc_final: 0.7962 (mtp85) REVERT: S 108 MET cc_start: 0.9489 (ptt) cc_final: 0.9065 (ppp) REVERT: S 111 LYS cc_start: 0.9273 (mmmt) cc_final: 0.8918 (mmmt) REVERT: T 1 MET cc_start: 0.9476 (mpp) cc_final: 0.8180 (tmm) REVERT: T 2 GLN cc_start: 0.9525 (mt0) cc_final: 0.9203 (mm-40) REVERT: T 26 PHE cc_start: 0.9695 (t80) cc_final: 0.9392 (t80) REVERT: T 32 GLN cc_start: 0.9146 (pt0) cc_final: 0.8884 (pt0) REVERT: T 35 LYS cc_start: 0.9734 (mttm) cc_final: 0.9506 (mmmm) REVERT: T 86 MET cc_start: 0.9710 (pmm) cc_final: 0.9370 (pmm) REVERT: T 108 MET cc_start: 0.9279 (tpt) cc_final: 0.8782 (tpt) REVERT: T 116 SER cc_start: 0.9332 (p) cc_final: 0.9021 (p) REVERT: T 120 PHE cc_start: 0.9476 (m-10) cc_final: 0.9207 (m-10) REVERT: T 127 GLU cc_start: 0.9543 (mm-30) cc_final: 0.9292 (mm-30) REVERT: T 129 HIS cc_start: 0.9311 (m90) cc_final: 0.9021 (m90) REVERT: U 2 GLN cc_start: 0.9452 (pm20) cc_final: 0.8937 (pp30) REVERT: U 24 GLN cc_start: 0.9562 (tt0) cc_final: 0.9117 (tm-30) REVERT: U 26 PHE cc_start: 0.9630 (t80) cc_final: 0.8999 (t80) REVERT: U 27 LEU cc_start: 0.9569 (tp) cc_final: 0.9004 (mt) REVERT: U 86 MET cc_start: 0.9860 (ptp) cc_final: 0.9645 (ptp) REVERT: U 102 ARG cc_start: 0.8301 (mtt180) cc_final: 0.8059 (mtp85) REVERT: V 23 ASN cc_start: 0.9641 (m-40) cc_final: 0.9410 (t0) REVERT: V 26 PHE cc_start: 0.9730 (t80) cc_final: 0.9234 (t80) REVERT: V 27 LEU cc_start: 0.9470 (mt) cc_final: 0.9043 (mt) REVERT: V 102 ARG cc_start: 0.8405 (mtt180) cc_final: 0.7890 (mtt-85) REVERT: V 108 MET cc_start: 0.9641 (ptm) cc_final: 0.9366 (ptp) REVERT: V 111 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8952 (mmmt) REVERT: V 120 PHE cc_start: 0.9474 (m-80) cc_final: 0.8916 (m-80) REVERT: V 138 LEU cc_start: 0.9332 (pp) cc_final: 0.9035 (pp) REVERT: V 139 ASP cc_start: 0.9375 (m-30) cc_final: 0.9083 (m-30) REVERT: W 2 GLN cc_start: 0.9587 (mt0) cc_final: 0.9344 (pm20) REVERT: W 23 ASN cc_start: 0.9672 (m-40) cc_final: 0.9384 (t0) REVERT: W 26 PHE cc_start: 0.9511 (t80) cc_final: 0.9135 (t80) REVERT: W 32 GLN cc_start: 0.9056 (pt0) cc_final: 0.8483 (pt0) REVERT: W 52 MET cc_start: 0.9411 (mtp) cc_final: 0.9203 (ttp) REVERT: W 56 GLU cc_start: 0.9507 (tt0) cc_final: 0.9101 (tp30) REVERT: W 102 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7538 (mtt180) REVERT: W 108 MET cc_start: 0.9283 (ptt) cc_final: 0.8647 (ppp) REVERT: W 111 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8832 (mmmt) REVERT: W 120 PHE cc_start: 0.9420 (m-80) cc_final: 0.8910 (m-80) REVERT: W 155 GLU cc_start: 0.9066 (tp30) cc_final: 0.8216 (tm-30) REVERT: X 1 MET cc_start: 0.9300 (mpp) cc_final: 0.8954 (mpp) REVERT: X 26 PHE cc_start: 0.9714 (t80) cc_final: 0.9267 (t80) REVERT: X 27 LEU cc_start: 0.9335 (mt) cc_final: 0.9033 (mt) REVERT: X 32 GLN cc_start: 0.9526 (pm20) cc_final: 0.8861 (pm20) REVERT: X 102 ARG cc_start: 0.8335 (mtt180) cc_final: 0.8109 (mtp85) REVERT: X 111 LYS cc_start: 0.9280 (mmpt) cc_final: 0.9027 (mmmt) outliers start: 10 outliers final: 2 residues processed: 1570 average time/residue: 0.5131 time to fit residues: 1187.3627 Evaluate side-chains 1251 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1249 time to evaluate : 3.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 219 optimal weight: 8.9990 chunk 328 optimal weight: 4.9990 chunk 347 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 311 optimal weight: 0.0050 chunk 93 optimal weight: 9.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS D 129 HIS E 34 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 HIS ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS I 130 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN M 76 HIS N 156 GLN O 34 HIS O 130 HIS P 76 HIS P 130 HIS Q 34 HIS Q 130 HIS Q 156 GLN R 130 HIS S 34 HIS S 130 HIS S 156 GLN T 32 GLN T 34 HIS ** T 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS V 130 HIS V 156 GLN W 34 HIS W 76 HIS W 129 HIS W 130 HIS X 34 HIS X 156 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 32072 Z= 0.183 Angle : 0.651 22.511 43500 Z= 0.310 Chirality : 0.038 0.195 4829 Planarity : 0.003 0.034 5615 Dihedral : 7.935 88.877 4222 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.42 % Allowed : 4.73 % Favored : 94.85 % 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: -0.38 (0.13), residues: 3742 helix: 0.34 (0.09), residues: 2963 sheet: None (None), residues: 0 loop : -2.28 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 37 HIS 0.008 0.001 HIS X 130 PHE 0.037 0.002 PHE Q 10 TYR 0.016 0.001 TYR U 25 ARG 0.005 0.001 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1623 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1609 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9085 (mpp) cc_final: 0.8240 (tmm) REVERT: A 26 PHE cc_start: 0.9665 (t80) cc_final: 0.9131 (t80) REVERT: A 71 TYR cc_start: 0.8936 (m-80) cc_final: 0.8725 (m-80) REVERT: A 86 MET cc_start: 0.9843 (ptp) cc_final: 0.9640 (ptp) REVERT: A 102 ARG cc_start: 0.8135 (mtt180) cc_final: 0.7476 (mtt180) REVERT: A 111 LYS cc_start: 0.9157 (mmpt) cc_final: 0.8880 (mmmt) REVERT: A 120 PHE cc_start: 0.9602 (m-10) cc_final: 0.9245 (m-80) REVERT: A 156 GLN cc_start: 0.5059 (tt0) cc_final: 0.4565 (mt0) REVERT: B 1 MET cc_start: 0.9190 (mpp) cc_final: 0.8538 (tmm) REVERT: B 2 GLN cc_start: 0.9529 (mt0) cc_final: 0.9098 (tp-100) REVERT: B 23 ASN cc_start: 0.9643 (m-40) cc_final: 0.9254 (p0) REVERT: B 26 PHE cc_start: 0.9511 (t80) cc_final: 0.9258 (t80) REVERT: B 56 GLU cc_start: 0.9523 (tt0) cc_final: 0.9208 (tp30) REVERT: B 73 ARG cc_start: 0.9038 (mtm110) cc_final: 0.8710 (mtm110) REVERT: B 86 MET cc_start: 0.9469 (pmm) cc_final: 0.9125 (pmm) REVERT: B 100 ARG cc_start: 0.9459 (mmt180) cc_final: 0.9202 (mmm160) REVERT: B 111 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8822 (mmmt) REVERT: B 120 PHE cc_start: 0.9493 (m-80) cc_final: 0.9159 (m-80) REVERT: B 127 GLU cc_start: 0.9466 (mm-30) cc_final: 0.9163 (mm-30) REVERT: B 129 HIS cc_start: 0.9298 (m90) cc_final: 0.9056 (m90) REVERT: B 154 ILE cc_start: 0.9664 (pt) cc_final: 0.9398 (mm) REVERT: C 26 PHE cc_start: 0.9701 (t80) cc_final: 0.9325 (t80) REVERT: C 27 LEU cc_start: 0.9462 (mt) cc_final: 0.8998 (mt) REVERT: C 100 ARG cc_start: 0.9376 (mmt180) cc_final: 0.9149 (mmm160) REVERT: C 102 ARG cc_start: 0.8500 (mtt180) cc_final: 0.8196 (mtp85) REVERT: C 111 LYS cc_start: 0.9167 (mmpt) cc_final: 0.8952 (mmmt) REVERT: C 120 PHE cc_start: 0.9350 (m-80) cc_final: 0.9033 (m-80) REVERT: C 123 ILE cc_start: 0.9577 (tt) cc_final: 0.9340 (tt) REVERT: C 130 HIS cc_start: 0.8977 (t-90) cc_final: 0.8626 (t-90) REVERT: C 139 ASP cc_start: 0.9267 (m-30) cc_final: 0.9064 (m-30) REVERT: D 1 MET cc_start: 0.9052 (mmp) cc_final: 0.8327 (tmm) REVERT: D 2 GLN cc_start: 0.9570 (mt0) cc_final: 0.9237 (pm20) REVERT: D 23 ASN cc_start: 0.9474 (m-40) cc_final: 0.8951 (m-40) REVERT: D 26 PHE cc_start: 0.9625 (t80) cc_final: 0.9258 (t80) REVERT: D 27 LEU cc_start: 0.9260 (mt) cc_final: 0.8943 (mt) REVERT: D 52 MET cc_start: 0.8873 (mtp) cc_final: 0.8587 (ttm) REVERT: D 111 LYS cc_start: 0.9200 (mmmt) cc_final: 0.8821 (mmmt) REVERT: D 120 PHE cc_start: 0.9436 (m-80) cc_final: 0.9003 (m-10) REVERT: D 123 ILE cc_start: 0.9283 (tt) cc_final: 0.9058 (tt) REVERT: D 139 ASP cc_start: 0.9419 (m-30) cc_final: 0.9001 (m-30) REVERT: D 156 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7037 (tm-30) REVERT: F 9 GLU cc_start: 0.9639 (tp30) cc_final: 0.9437 (tp30) REVERT: F 23 ASN cc_start: 0.9780 (m-40) cc_final: 0.9518 (t0) REVERT: F 26 PHE cc_start: 0.9658 (t80) cc_final: 0.9157 (t80) REVERT: F 56 GLU cc_start: 0.9639 (tt0) cc_final: 0.9371 (tp30) REVERT: F 60 ASP cc_start: 0.9827 (p0) cc_final: 0.9559 (p0) REVERT: F 71 TYR cc_start: 0.9449 (m-10) cc_final: 0.8514 (m-80) REVERT: F 86 MET cc_start: 0.9478 (pmm) cc_final: 0.9186 (pmm) REVERT: F 102 ARG cc_start: 0.8415 (mtt180) cc_final: 0.8154 (mtp85) REVERT: F 105 ILE cc_start: 0.9631 (mt) cc_final: 0.9425 (mp) REVERT: F 108 MET cc_start: 0.9382 (ptt) cc_final: 0.8724 (ppp) REVERT: F 111 LYS cc_start: 0.9295 (mmmt) cc_final: 0.8932 (mmmt) REVERT: F 129 HIS cc_start: 0.9351 (m90) cc_final: 0.9147 (m90) REVERT: E 6 GLU cc_start: 0.9561 (tp30) cc_final: 0.9300 (tp30) REVERT: E 26 PHE cc_start: 0.9627 (t80) cc_final: 0.9047 (t80) REVERT: E 27 LEU cc_start: 0.9150 (mt) cc_final: 0.8878 (mm) REVERT: E 86 MET cc_start: 0.9539 (pmm) cc_final: 0.9238 (pmm) REVERT: E 102 ARG cc_start: 0.8267 (mtt180) cc_final: 0.7781 (mtp85) REVERT: E 111 LYS cc_start: 0.9306 (mmmt) cc_final: 0.8941 (mmmt) REVERT: E 120 PHE cc_start: 0.9460 (m-10) cc_final: 0.9224 (m-80) REVERT: E 129 HIS cc_start: 0.9348 (m90) cc_final: 0.9136 (m90) REVERT: G 2 GLN cc_start: 0.9528 (mt0) cc_final: 0.9205 (pm20) REVERT: G 23 ASN cc_start: 0.9717 (m-40) cc_final: 0.9373 (t0) REVERT: G 35 LYS cc_start: 0.9799 (mmmm) cc_final: 0.9489 (mmmm) REVERT: G 86 MET cc_start: 0.9601 (pmm) cc_final: 0.9372 (pmm) REVERT: G 102 ARG cc_start: 0.8064 (mtt180) cc_final: 0.7831 (mtp85) REVERT: G 120 PHE cc_start: 0.9431 (m-10) cc_final: 0.9065 (m-10) REVERT: G 123 ILE cc_start: 0.9543 (mm) cc_final: 0.9184 (mm) REVERT: G 127 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9123 (mm-30) REVERT: G 139 ASP cc_start: 0.9308 (m-30) cc_final: 0.9012 (m-30) REVERT: G 153 VAL cc_start: 0.9818 (m) cc_final: 0.9593 (p) REVERT: G 154 ILE cc_start: 0.9590 (pt) cc_final: 0.9349 (mt) REVERT: H 1 MET cc_start: 0.9356 (mpp) cc_final: 0.9138 (mpp) REVERT: H 23 ASN cc_start: 0.9680 (m-40) cc_final: 0.9444 (t0) REVERT: H 26 PHE cc_start: 0.9623 (t80) cc_final: 0.9279 (t80) REVERT: H 35 LYS cc_start: 0.9812 (mmmm) cc_final: 0.9501 (mmmm) REVERT: H 52 MET cc_start: 0.8591 (mtt) cc_final: 0.8213 (mtt) REVERT: H 86 MET cc_start: 0.9541 (pmm) cc_final: 0.9301 (pmm) REVERT: H 111 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8861 (mmmt) REVERT: H 116 SER cc_start: 0.9616 (m) cc_final: 0.9387 (p) REVERT: H 139 ASP cc_start: 0.9563 (m-30) cc_final: 0.9361 (m-30) REVERT: I 2 GLN cc_start: 0.9578 (mt0) cc_final: 0.9275 (mm-40) REVERT: I 9 GLU cc_start: 0.9654 (tp30) cc_final: 0.9422 (tp30) REVERT: I 23 ASN cc_start: 0.9650 (m-40) cc_final: 0.9301 (t0) REVERT: I 24 GLN cc_start: 0.9481 (tt0) cc_final: 0.9205 (tm-30) REVERT: I 26 PHE cc_start: 0.9651 (t80) cc_final: 0.9282 (t80) REVERT: I 27 LEU cc_start: 0.9354 (mt) cc_final: 0.9127 (mt) REVERT: I 71 TYR cc_start: 0.9343 (m-80) cc_final: 0.9060 (m-80) REVERT: I 86 MET cc_start: 0.9613 (pmm) cc_final: 0.9363 (pmm) REVERT: I 111 LYS cc_start: 0.9242 (mmpt) cc_final: 0.8963 (mmmt) REVERT: I 120 PHE cc_start: 0.9371 (m-80) cc_final: 0.8808 (m-80) REVERT: J 23 ASN cc_start: 0.9399 (m-40) cc_final: 0.9196 (t0) REVERT: J 26 PHE cc_start: 0.9607 (t80) cc_final: 0.9390 (t80) REVERT: J 120 PHE cc_start: 0.9428 (m-80) cc_final: 0.9089 (m-80) REVERT: K 2 GLN cc_start: 0.9589 (mt0) cc_final: 0.9385 (pm20) REVERT: K 26 PHE cc_start: 0.9636 (t80) cc_final: 0.9308 (t80) REVERT: K 99 ASP cc_start: 0.8942 (p0) cc_final: 0.8678 (p0) REVERT: K 100 ARG cc_start: 0.9409 (mmt-90) cc_final: 0.9159 (mmm160) REVERT: K 111 LYS cc_start: 0.9223 (mmpt) cc_final: 0.8937 (mmmt) REVERT: K 120 PHE cc_start: 0.9360 (m-80) cc_final: 0.9048 (m-80) REVERT: K 126 ASP cc_start: 0.9327 (m-30) cc_final: 0.9109 (m-30) REVERT: K 139 ASP cc_start: 0.9325 (m-30) cc_final: 0.9081 (m-30) REVERT: L 1 MET cc_start: 0.9382 (mmp) cc_final: 0.9042 (mmp) REVERT: L 23 ASN cc_start: 0.9642 (m-40) cc_final: 0.9252 (m-40) REVERT: L 26 PHE cc_start: 0.9663 (t80) cc_final: 0.9259 (t80) REVERT: L 27 LEU cc_start: 0.9453 (mt) cc_final: 0.8954 (mt) REVERT: L 34 HIS cc_start: 0.9209 (t70) cc_final: 0.8874 (t-90) REVERT: L 35 LYS cc_start: 0.9786 (mmtp) cc_final: 0.9557 (mmmm) REVERT: L 52 MET cc_start: 0.9555 (mtp) cc_final: 0.8576 (mtp) REVERT: L 53 ARG cc_start: 0.9206 (ttp-110) cc_final: 0.8928 (ptp-110) REVERT: L 102 ARG cc_start: 0.8322 (mtt180) cc_final: 0.7910 (mtp85) REVERT: L 111 LYS cc_start: 0.9274 (mmpt) cc_final: 0.8982 (mmmt) REVERT: L 130 HIS cc_start: 0.9036 (t-90) cc_final: 0.8737 (t-170) REVERT: L 139 ASP cc_start: 0.9267 (m-30) cc_final: 0.9055 (m-30) REVERT: M 1 MET cc_start: 0.9067 (mmm) cc_final: 0.8248 (tmm) REVERT: M 2 GLN cc_start: 0.9596 (mt0) cc_final: 0.9023 (pp30) REVERT: M 23 ASN cc_start: 0.9567 (m-40) cc_final: 0.9238 (t0) REVERT: M 26 PHE cc_start: 0.9595 (t80) cc_final: 0.9303 (t80) REVERT: M 27 LEU cc_start: 0.9374 (mt) cc_final: 0.8946 (mt) REVERT: M 86 MET cc_start: 0.9497 (pmm) cc_final: 0.9244 (pmm) REVERT: M 111 LYS cc_start: 0.9078 (mmpt) cc_final: 0.8835 (mmmt) REVERT: M 120 PHE cc_start: 0.9630 (m-80) cc_final: 0.9272 (m-10) REVERT: M 123 ILE cc_start: 0.9161 (tt) cc_final: 0.8915 (tt) REVERT: M 155 GLU cc_start: 0.9123 (tp30) cc_final: 0.8616 (mp0) REVERT: M 156 GLN cc_start: 0.7919 (tt0) cc_final: 0.6201 (tt0) REVERT: N 2 GLN cc_start: 0.9535 (mt0) cc_final: 0.9259 (pm20) REVERT: N 23 ASN cc_start: 0.9552 (m-40) cc_final: 0.9265 (t0) REVERT: N 27 LEU cc_start: 0.9390 (mt) cc_final: 0.9072 (mt) REVERT: N 34 HIS cc_start: 0.8151 (p90) cc_final: 0.7886 (p90) REVERT: N 86 MET cc_start: 0.9486 (pmm) cc_final: 0.9265 (pmm) REVERT: N 102 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7571 (mtp85) REVERT: N 108 MET cc_start: 0.9210 (ptt) cc_final: 0.8351 (ppp) REVERT: N 111 LYS cc_start: 0.9088 (mmpt) cc_final: 0.8809 (mmmt) REVERT: N 120 PHE cc_start: 0.9178 (m-80) cc_final: 0.8951 (m-80) REVERT: N 123 ILE cc_start: 0.9539 (mm) cc_final: 0.9320 (mm) REVERT: N 127 GLU cc_start: 0.9422 (mm-30) cc_final: 0.9205 (mm-30) REVERT: N 129 HIS cc_start: 0.9616 (m-70) cc_final: 0.9297 (m-70) REVERT: N 139 ASP cc_start: 0.9412 (m-30) cc_final: 0.9157 (m-30) REVERT: O 26 PHE cc_start: 0.9552 (t80) cc_final: 0.8939 (t80) REVERT: O 27 LEU cc_start: 0.9309 (mp) cc_final: 0.9052 (mp) REVERT: O 32 GLN cc_start: 0.9259 (pt0) cc_final: 0.9011 (pt0) REVERT: O 102 ARG cc_start: 0.8559 (mtt180) cc_final: 0.7800 (mtt180) REVERT: O 111 LYS cc_start: 0.9189 (mmpt) cc_final: 0.8926 (mmmt) REVERT: O 139 ASP cc_start: 0.9345 (m-30) cc_final: 0.9124 (m-30) REVERT: O 156 GLN cc_start: 0.7266 (pp30) cc_final: 0.6993 (pp30) REVERT: P 1 MET cc_start: 0.9134 (mpp) cc_final: 0.8461 (tmm) REVERT: P 2 GLN cc_start: 0.9482 (pm20) cc_final: 0.9266 (pm20) REVERT: P 23 ASN cc_start: 0.9822 (m-40) cc_final: 0.9576 (m-40) REVERT: P 26 PHE cc_start: 0.9438 (t80) cc_final: 0.8867 (t80) REVERT: P 27 LEU cc_start: 0.9349 (mt) cc_final: 0.8923 (mt) REVERT: P 32 GLN cc_start: 0.9590 (pm20) cc_final: 0.9195 (pm20) REVERT: P 56 GLU cc_start: 0.9741 (pp20) cc_final: 0.9538 (tp30) REVERT: P 102 ARG cc_start: 0.8331 (mtt180) cc_final: 0.8071 (mtp85) REVERT: P 109 ARG cc_start: 0.9044 (mtp180) cc_final: 0.8834 (tpm170) REVERT: P 111 LYS cc_start: 0.9222 (mmpt) cc_final: 0.9015 (mmmt) REVERT: P 120 PHE cc_start: 0.9632 (m-10) cc_final: 0.9359 (m-80) REVERT: P 130 HIS cc_start: 0.9076 (t-90) cc_final: 0.8751 (t-90) REVERT: P 139 ASP cc_start: 0.9270 (m-30) cc_final: 0.9044 (m-30) REVERT: Q 23 ASN cc_start: 0.9698 (m-40) cc_final: 0.9227 (m-40) REVERT: Q 26 PHE cc_start: 0.9630 (t80) cc_final: 0.9026 (t80) REVERT: Q 27 LEU cc_start: 0.9422 (mt) cc_final: 0.9035 (mt) REVERT: Q 39 LYS cc_start: 0.9676 (mtmm) cc_final: 0.9472 (mtmm) REVERT: Q 56 GLU cc_start: 0.9574 (tm-30) cc_final: 0.9354 (tp30) REVERT: Q 102 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7784 (mtp85) REVERT: Q 120 PHE cc_start: 0.9522 (m-10) cc_final: 0.9242 (m-10) REVERT: Q 139 ASP cc_start: 0.9349 (m-30) cc_final: 0.9124 (m-30) REVERT: R 27 LEU cc_start: 0.9553 (tt) cc_final: 0.9248 (mt) REVERT: R 45 ARG cc_start: 0.9029 (mtp85) cc_final: 0.8625 (mmm-85) REVERT: R 49 PHE cc_start: 0.9665 (m-80) cc_final: 0.9387 (m-80) REVERT: R 52 MET cc_start: 0.9567 (mtm) cc_final: 0.9112 (mtm) REVERT: R 56 GLU cc_start: 0.9431 (tt0) cc_final: 0.9134 (tp30) REVERT: R 111 LYS cc_start: 0.9288 (mmpt) cc_final: 0.9020 (mmmt) REVERT: R 127 GLU cc_start: 0.9521 (mm-30) cc_final: 0.9268 (mm-30) REVERT: R 155 GLU cc_start: 0.9064 (tp30) cc_final: 0.8326 (tm-30) REVERT: S 23 ASN cc_start: 0.9615 (m-40) cc_final: 0.9189 (t0) REVERT: S 26 PHE cc_start: 0.9648 (t80) cc_final: 0.9352 (t80) REVERT: S 27 LEU cc_start: 0.9196 (mt) cc_final: 0.8883 (mt) REVERT: S 86 MET cc_start: 0.9719 (ptp) cc_final: 0.9451 (ptp) REVERT: S 100 ARG cc_start: 0.9106 (mmt-90) cc_final: 0.8821 (mmm160) REVERT: S 102 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7911 (mtp85) REVERT: S 111 LYS cc_start: 0.9254 (mmmt) cc_final: 0.8888 (mmmt) REVERT: T 2 GLN cc_start: 0.9484 (mt0) cc_final: 0.9180 (mm-40) REVERT: T 10 PHE cc_start: 0.9428 (m-80) cc_final: 0.9155 (m-80) REVERT: T 26 PHE cc_start: 0.9678 (t80) cc_final: 0.9416 (t80) REVERT: T 27 LEU cc_start: 0.9269 (mt) cc_final: 0.9058 (mt) REVERT: T 32 GLN cc_start: 0.9198 (pt0) cc_final: 0.8760 (pt0) REVERT: T 108 MET cc_start: 0.9297 (tpt) cc_final: 0.8731 (tpt) REVERT: T 120 PHE cc_start: 0.9463 (m-10) cc_final: 0.9135 (m-10) REVERT: T 129 HIS cc_start: 0.9390 (m90) cc_final: 0.9120 (m90) REVERT: U 24 GLN cc_start: 0.9618 (tt0) cc_final: 0.9258 (tp-100) REVERT: U 26 PHE cc_start: 0.9612 (t80) cc_final: 0.8900 (t80) REVERT: U 27 LEU cc_start: 0.9550 (tp) cc_final: 0.8940 (mt) REVERT: U 86 MET cc_start: 0.9828 (ptp) cc_final: 0.9536 (ptp) REVERT: U 105 ILE cc_start: 0.9647 (mt) cc_final: 0.9428 (mt) REVERT: U 108 MET cc_start: 0.9342 (ptt) cc_final: 0.8845 (ppp) REVERT: U 109 ARG cc_start: 0.9522 (mtp85) cc_final: 0.9278 (mtp85) REVERT: U 120 PHE cc_start: 0.9333 (m-80) cc_final: 0.9063 (m-80) REVERT: V 23 ASN cc_start: 0.9631 (m-40) cc_final: 0.9408 (t0) REVERT: V 26 PHE cc_start: 0.9701 (t80) cc_final: 0.9154 (t80) REVERT: V 27 LEU cc_start: 0.9430 (mt) cc_final: 0.8928 (mt) REVERT: V 120 PHE cc_start: 0.9528 (m-80) cc_final: 0.8976 (m-80) REVERT: V 139 ASP cc_start: 0.9308 (m-30) cc_final: 0.8969 (m-30) REVERT: W 2 GLN cc_start: 0.9557 (mt0) cc_final: 0.9293 (pm20) REVERT: W 23 ASN cc_start: 0.9619 (m-40) cc_final: 0.9343 (t0) REVERT: W 26 PHE cc_start: 0.9453 (t80) cc_final: 0.9033 (t80) REVERT: W 52 MET cc_start: 0.9384 (mtp) cc_final: 0.9047 (ttp) REVERT: W 56 GLU cc_start: 0.9464 (tt0) cc_final: 0.9052 (tp30) REVERT: W 60 ASP cc_start: 0.9598 (m-30) cc_final: 0.9318 (m-30) REVERT: W 102 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7881 (mtp85) REVERT: W 108 MET cc_start: 0.9201 (ptt) cc_final: 0.8647 (ppp) REVERT: W 111 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8863 (mmmt) REVERT: W 120 PHE cc_start: 0.9474 (m-80) cc_final: 0.8963 (m-80) REVERT: W 155 GLU cc_start: 0.8962 (tp30) cc_final: 0.8127 (tm-30) REVERT: X 23 ASN cc_start: 0.9723 (m-40) cc_final: 0.9498 (m-40) REVERT: X 26 PHE cc_start: 0.9673 (t80) cc_final: 0.9205 (t80) REVERT: X 27 LEU cc_start: 0.9300 (mt) cc_final: 0.8880 (mt) REVERT: X 60 ASP cc_start: 0.9882 (p0) cc_final: 0.9679 (p0) REVERT: X 102 ARG cc_start: 0.8296 (mtt180) cc_final: 0.8095 (mtp85) REVERT: X 111 LYS cc_start: 0.9239 (mmpt) cc_final: 0.8983 (mmmt) REVERT: X 120 PHE cc_start: 0.9423 (m-80) cc_final: 0.9135 (m-10) outliers start: 14 outliers final: 5 residues processed: 1616 average time/residue: 0.5093 time to fit residues: 1218.7230 Evaluate side-chains 1272 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1267 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 296 optimal weight: 20.0000 chunk 240 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 312 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 129 HIS ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS F 130 HIS E 34 HIS E 130 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS H 130 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 HIS ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN ** N 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS P 118 ASN Q 34 HIS Q 130 HIS Q 156 GLN ** R 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 HIS S 130 HIS S 156 GLN ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 76 HIS T 156 GLN U 112 HIS ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 156 GLN W 34 HIS W 129 HIS W 130 HIS ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32072 Z= 0.246 Angle : 0.720 18.798 43500 Z= 0.351 Chirality : 0.039 0.210 4829 Planarity : 0.004 0.051 5615 Dihedral : 8.027 89.556 4222 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.18 % Allowed : 4.61 % Favored : 95.21 % 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: -0.46 (0.13), residues: 3742 helix: 0.25 (0.09), residues: 3032 sheet: None (None), residues: 0 loop : -2.40 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 37 HIS 0.011 0.001 HIS K 34 PHE 0.052 0.003 PHE D 10 TYR 0.020 0.002 TYR P 71 ARG 0.006 0.001 ARG N 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1516 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1510 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.9787 (m-40) cc_final: 0.9425 (m-40) REVERT: A 26 PHE cc_start: 0.9669 (t80) cc_final: 0.9115 (t80) REVERT: A 27 LEU cc_start: 0.9238 (mt) cc_final: 0.8799 (mt) REVERT: A 71 TYR cc_start: 0.8868 (m-80) cc_final: 0.8636 (m-80) REVERT: A 111 LYS cc_start: 0.9137 (mmpt) cc_final: 0.8858 (mmmt) REVERT: A 120 PHE cc_start: 0.9077 (m-10) cc_final: 0.8850 (m-10) REVERT: A 138 LEU cc_start: 0.9528 (pp) cc_final: 0.9326 (pp) REVERT: B 1 MET cc_start: 0.9263 (mpp) cc_final: 0.8671 (tmm) REVERT: B 2 GLN cc_start: 0.9511 (mt0) cc_final: 0.9223 (pm20) REVERT: B 23 ASN cc_start: 0.9586 (m-40) cc_final: 0.9225 (m-40) REVERT: B 26 PHE cc_start: 0.9474 (t80) cc_final: 0.9001 (t80) REVERT: B 27 LEU cc_start: 0.9079 (mt) cc_final: 0.8600 (mt) REVERT: B 35 LYS cc_start: 0.9769 (mtpp) cc_final: 0.9507 (mmmm) REVERT: B 43 TYR cc_start: 0.9593 (t80) cc_final: 0.9372 (m-80) REVERT: B 56 GLU cc_start: 0.9518 (tt0) cc_final: 0.9226 (tp30) REVERT: B 86 MET cc_start: 0.9486 (pmm) cc_final: 0.9183 (pmm) REVERT: B 100 ARG cc_start: 0.9437 (mmt180) cc_final: 0.9158 (mmm160) REVERT: B 120 PHE cc_start: 0.9525 (m-80) cc_final: 0.9221 (m-80) REVERT: B 127 GLU cc_start: 0.9558 (mm-30) cc_final: 0.9223 (mm-30) REVERT: B 129 HIS cc_start: 0.9389 (m90) cc_final: 0.9162 (m90) REVERT: B 154 ILE cc_start: 0.9635 (pt) cc_final: 0.9344 (mm) REVERT: C 26 PHE cc_start: 0.9683 (t80) cc_final: 0.9295 (t80) REVERT: C 27 LEU cc_start: 0.9473 (mt) cc_final: 0.9009 (mt) REVERT: C 33 ASP cc_start: 0.9002 (p0) cc_final: 0.8786 (p0) REVERT: C 100 ARG cc_start: 0.9393 (mmt180) cc_final: 0.9149 (mmm160) REVERT: C 102 ARG cc_start: 0.8512 (mtt180) cc_final: 0.8200 (mtp85) REVERT: C 108 MET cc_start: 0.9715 (ptp) cc_final: 0.9410 (ptp) REVERT: C 111 LYS cc_start: 0.9239 (mmpt) cc_final: 0.8961 (mmmt) REVERT: C 120 PHE cc_start: 0.9531 (m-80) cc_final: 0.9056 (m-80) REVERT: C 123 ILE cc_start: 0.9517 (tt) cc_final: 0.8941 (tt) REVERT: C 130 HIS cc_start: 0.9219 (t-90) cc_final: 0.8899 (t-90) REVERT: D 1 MET cc_start: 0.9206 (mmp) cc_final: 0.8457 (tmm) REVERT: D 2 GLN cc_start: 0.9627 (mt0) cc_final: 0.9293 (pm20) REVERT: D 27 LEU cc_start: 0.9247 (mt) cc_final: 0.8976 (mt) REVERT: D 120 PHE cc_start: 0.9500 (m-80) cc_final: 0.9067 (m-80) REVERT: D 123 ILE cc_start: 0.9244 (tt) cc_final: 0.8939 (tt) REVERT: F 23 ASN cc_start: 0.9712 (m-40) cc_final: 0.9225 (t0) REVERT: F 26 PHE cc_start: 0.9595 (t80) cc_final: 0.9236 (t80) REVERT: F 27 LEU cc_start: 0.9381 (mm) cc_final: 0.8332 (mm) REVERT: F 33 ASP cc_start: 0.9177 (p0) cc_final: 0.8967 (p0) REVERT: F 56 GLU cc_start: 0.9624 (tt0) cc_final: 0.9409 (tp30) REVERT: F 60 ASP cc_start: 0.9850 (p0) cc_final: 0.9513 (p0) REVERT: F 111 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8918 (mmmt) REVERT: E 26 PHE cc_start: 0.9633 (t80) cc_final: 0.9225 (t80) REVERT: E 120 PHE cc_start: 0.9515 (m-10) cc_final: 0.9303 (m-10) REVERT: E 127 GLU cc_start: 0.9592 (mm-30) cc_final: 0.9311 (pt0) REVERT: E 129 HIS cc_start: 0.9403 (m90) cc_final: 0.9166 (m90) REVERT: E 130 HIS cc_start: 0.9296 (t70) cc_final: 0.9020 (t70) REVERT: G 2 GLN cc_start: 0.9561 (mt0) cc_final: 0.9306 (pm20) REVERT: G 26 PHE cc_start: 0.9534 (t80) cc_final: 0.9154 (t80) REVERT: G 27 LEU cc_start: 0.9223 (mt) cc_final: 0.8816 (mt) REVERT: G 52 MET cc_start: 0.9256 (mtm) cc_final: 0.8853 (mtm) REVERT: G 108 MET cc_start: 0.9682 (mtm) cc_final: 0.9154 (tmm) REVERT: G 109 ARG cc_start: 0.9215 (mmt180) cc_final: 0.8849 (ttt180) REVERT: G 123 ILE cc_start: 0.9519 (mm) cc_final: 0.9245 (mm) REVERT: G 127 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9180 (mm-30) REVERT: G 139 ASP cc_start: 0.9341 (m-30) cc_final: 0.9076 (m-30) REVERT: H 1 MET cc_start: 0.9496 (mpp) cc_final: 0.8949 (mpp) REVERT: H 23 ASN cc_start: 0.9666 (m-40) cc_final: 0.9244 (t0) REVERT: H 26 PHE cc_start: 0.9629 (t80) cc_final: 0.9154 (t80) REVERT: H 27 LEU cc_start: 0.9249 (mt) cc_final: 0.8606 (mt) REVERT: H 35 LYS cc_start: 0.9806 (mmmm) cc_final: 0.9534 (mmmm) REVERT: H 100 ARG cc_start: 0.9188 (mmp80) cc_final: 0.8987 (mmm160) REVERT: H 111 LYS cc_start: 0.9152 (mmmt) cc_final: 0.8822 (mmmt) REVERT: H 139 ASP cc_start: 0.9558 (m-30) cc_final: 0.9340 (m-30) REVERT: I 2 GLN cc_start: 0.9598 (mt0) cc_final: 0.9370 (mm-40) REVERT: I 9 GLU cc_start: 0.9659 (tp30) cc_final: 0.9421 (tp30) REVERT: I 23 ASN cc_start: 0.9655 (m-40) cc_final: 0.9175 (t0) REVERT: I 24 GLN cc_start: 0.9537 (tt0) cc_final: 0.9188 (tm-30) REVERT: I 26 PHE cc_start: 0.9658 (t80) cc_final: 0.9163 (t80) REVERT: I 27 LEU cc_start: 0.9364 (mt) cc_final: 0.8621 (mt) REVERT: I 111 LYS cc_start: 0.9247 (mmpt) cc_final: 0.8976 (mmmt) REVERT: I 120 PHE cc_start: 0.9449 (m-80) cc_final: 0.9014 (m-80) REVERT: J 26 PHE cc_start: 0.9642 (t80) cc_final: 0.9418 (t80) REVERT: J 52 MET cc_start: 0.8906 (mtm) cc_final: 0.8307 (mtm) REVERT: J 120 PHE cc_start: 0.9447 (m-80) cc_final: 0.9095 (m-80) REVERT: K 2 GLN cc_start: 0.9593 (mt0) cc_final: 0.9375 (pm20) REVERT: K 100 ARG cc_start: 0.9376 (mmt-90) cc_final: 0.9150 (mmm160) REVERT: K 111 LYS cc_start: 0.9187 (mmpt) cc_final: 0.8904 (mmmt) REVERT: K 120 PHE cc_start: 0.9479 (m-80) cc_final: 0.8983 (m-80) REVERT: L 10 PHE cc_start: 0.9529 (m-80) cc_final: 0.9255 (m-80) REVERT: L 23 ASN cc_start: 0.9643 (m-40) cc_final: 0.9143 (m-40) REVERT: L 26 PHE cc_start: 0.9675 (t80) cc_final: 0.9150 (t80) REVERT: L 27 LEU cc_start: 0.9510 (mt) cc_final: 0.8795 (mt) REVERT: L 34 HIS cc_start: 0.9261 (t70) cc_final: 0.8964 (t-90) REVERT: L 52 MET cc_start: 0.9576 (mtp) cc_final: 0.8585 (mtp) REVERT: L 53 ARG cc_start: 0.9237 (ttp-110) cc_final: 0.8963 (ptp-110) REVERT: L 111 LYS cc_start: 0.9204 (mmpt) cc_final: 0.8930 (mmmt) REVERT: L 120 PHE cc_start: 0.9212 (m-80) cc_final: 0.8998 (m-80) REVERT: L 130 HIS cc_start: 0.9150 (t-90) cc_final: 0.8855 (t-170) REVERT: M 1 MET cc_start: 0.9154 (mmm) cc_final: 0.8290 (tmm) REVERT: M 2 GLN cc_start: 0.9586 (mt0) cc_final: 0.8986 (pp30) REVERT: M 26 PHE cc_start: 0.9618 (t80) cc_final: 0.9356 (t80) REVERT: M 27 LEU cc_start: 0.9436 (mt) cc_final: 0.9065 (mt) REVERT: M 101 LEU cc_start: 0.9564 (mt) cc_final: 0.9360 (mt) REVERT: M 120 PHE cc_start: 0.9522 (m-80) cc_final: 0.9169 (m-10) REVERT: M 130 HIS cc_start: 0.9426 (t-170) cc_final: 0.9076 (t-170) REVERT: M 139 ASP cc_start: 0.9516 (m-30) cc_final: 0.9258 (m-30) REVERT: M 155 GLU cc_start: 0.9104 (tp30) cc_final: 0.8610 (mp0) REVERT: M 156 GLN cc_start: 0.7327 (tt0) cc_final: 0.5606 (tt0) REVERT: N 2 GLN cc_start: 0.9561 (mt0) cc_final: 0.9276 (pm20) REVERT: N 26 PHE cc_start: 0.9516 (t80) cc_final: 0.9195 (t80) REVERT: N 27 LEU cc_start: 0.9411 (mt) cc_final: 0.9163 (mt) REVERT: N 34 HIS cc_start: 0.8265 (p90) cc_final: 0.7952 (p90) REVERT: N 35 LYS cc_start: 0.9585 (tptp) cc_final: 0.9337 (tppt) REVERT: N 43 TYR cc_start: 0.9648 (t80) cc_final: 0.9362 (t80) REVERT: N 86 MET cc_start: 0.9583 (pmm) cc_final: 0.9371 (pmm) REVERT: N 108 MET cc_start: 0.9311 (ptt) cc_final: 0.8486 (ppp) REVERT: N 111 LYS cc_start: 0.9074 (mmpt) cc_final: 0.8807 (mmmt) REVERT: N 120 PHE cc_start: 0.9471 (m-80) cc_final: 0.9054 (m-80) REVERT: N 129 HIS cc_start: 0.9634 (m-70) cc_final: 0.9348 (m90) REVERT: N 139 ASP cc_start: 0.9477 (m-30) cc_final: 0.9246 (m-30) REVERT: O 10 PHE cc_start: 0.9541 (m-80) cc_final: 0.9168 (m-80) REVERT: O 25 TYR cc_start: 0.9514 (m-10) cc_final: 0.9288 (m-10) REVERT: O 26 PHE cc_start: 0.9558 (t80) cc_final: 0.9163 (t80) REVERT: O 27 LEU cc_start: 0.9356 (mp) cc_final: 0.8913 (mp) REVERT: O 32 GLN cc_start: 0.9343 (pt0) cc_final: 0.9090 (pt0) REVERT: O 130 HIS cc_start: 0.9635 (t-90) cc_final: 0.9370 (t-170) REVERT: P 23 ASN cc_start: 0.9791 (m-40) cc_final: 0.9532 (m-40) REVERT: P 26 PHE cc_start: 0.9419 (t80) cc_final: 0.8831 (t80) REVERT: P 27 LEU cc_start: 0.9404 (mt) cc_final: 0.8900 (mt) REVERT: P 111 LYS cc_start: 0.9160 (mmpt) cc_final: 0.8920 (mmmt) REVERT: P 139 ASP cc_start: 0.9268 (m-30) cc_final: 0.9048 (m-30) REVERT: Q 23 ASN cc_start: 0.9693 (m-40) cc_final: 0.9151 (m-40) REVERT: Q 26 PHE cc_start: 0.9626 (t80) cc_final: 0.8982 (t80) REVERT: Q 27 LEU cc_start: 0.9444 (mt) cc_final: 0.8987 (mt) REVERT: Q 43 TYR cc_start: 0.9752 (t80) cc_final: 0.9381 (t80) REVERT: Q 56 GLU cc_start: 0.9548 (tm-30) cc_final: 0.9325 (tp30) REVERT: Q 111 LYS cc_start: 0.9104 (mmpt) cc_final: 0.8854 (mmmt) REVERT: Q 120 PHE cc_start: 0.9548 (m-10) cc_final: 0.9323 (m-10) REVERT: R 27 LEU cc_start: 0.9622 (tt) cc_final: 0.9239 (mt) REVERT: R 40 LEU cc_start: 0.9832 (tp) cc_final: 0.9628 (tp) REVERT: R 45 ARG cc_start: 0.8982 (mtp85) cc_final: 0.8546 (mmm-85) REVERT: R 49 PHE cc_start: 0.9694 (m-80) cc_final: 0.9449 (m-80) REVERT: R 52 MET cc_start: 0.9620 (mtm) cc_final: 0.9274 (mtm) REVERT: R 56 GLU cc_start: 0.9443 (tt0) cc_final: 0.9173 (tp30) REVERT: R 111 LYS cc_start: 0.9292 (mmpt) cc_final: 0.9044 (mmmt) REVERT: R 127 GLU cc_start: 0.9563 (mm-30) cc_final: 0.9276 (mm-30) REVERT: R 139 ASP cc_start: 0.9472 (m-30) cc_final: 0.9242 (m-30) REVERT: R 155 GLU cc_start: 0.9069 (tp30) cc_final: 0.8403 (tm-30) REVERT: S 26 PHE cc_start: 0.9672 (t80) cc_final: 0.9429 (t80) REVERT: S 27 LEU cc_start: 0.9289 (mt) cc_final: 0.8993 (mt) REVERT: S 102 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7950 (mtp85) REVERT: S 111 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8934 (mmmt) REVERT: S 120 PHE cc_start: 0.9255 (m-80) cc_final: 0.8801 (m-80) REVERT: S 143 LYS cc_start: 0.9148 (tmmt) cc_final: 0.8861 (tmtt) REVERT: T 2 GLN cc_start: 0.9510 (mt0) cc_final: 0.9182 (mm-40) REVERT: T 26 PHE cc_start: 0.9657 (t80) cc_final: 0.9320 (t80) REVERT: T 27 LEU cc_start: 0.9310 (mt) cc_final: 0.8810 (mt) REVERT: T 32 GLN cc_start: 0.9725 (mt0) cc_final: 0.9426 (pt0) REVERT: T 86 MET cc_start: 0.9742 (pmm) cc_final: 0.9460 (pmm) REVERT: T 100 ARG cc_start: 0.9539 (mmm160) cc_final: 0.9274 (mmm-85) REVERT: T 108 MET cc_start: 0.9321 (tpt) cc_final: 0.8730 (tpt) REVERT: T 120 PHE cc_start: 0.9497 (m-10) cc_final: 0.9218 (m-10) REVERT: T 129 HIS cc_start: 0.9440 (m90) cc_final: 0.9165 (m90) REVERT: T 138 LEU cc_start: 0.9348 (pp) cc_final: 0.9082 (pp) REVERT: T 139 ASP cc_start: 0.9464 (m-30) cc_final: 0.9227 (m-30) REVERT: U 26 PHE cc_start: 0.9615 (t80) cc_final: 0.9000 (t80) REVERT: U 27 LEU cc_start: 0.9582 (tp) cc_final: 0.9088 (mt) REVERT: U 86 MET cc_start: 0.9853 (ptp) cc_final: 0.9646 (ptp) REVERT: U 108 MET cc_start: 0.9399 (ptt) cc_final: 0.8909 (ppp) REVERT: U 120 PHE cc_start: 0.9428 (m-80) cc_final: 0.9107 (m-80) REVERT: U 156 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8032 (tm-30) REVERT: V 10 PHE cc_start: 0.9530 (m-80) cc_final: 0.9249 (m-80) REVERT: V 23 ASN cc_start: 0.9635 (m-40) cc_final: 0.9350 (t0) REVERT: V 26 PHE cc_start: 0.9684 (t80) cc_final: 0.9034 (t80) REVERT: V 27 LEU cc_start: 0.9474 (mt) cc_final: 0.8807 (mt) REVERT: V 71 TYR cc_start: 0.9003 (m-80) cc_final: 0.8722 (m-10) REVERT: V 111 LYS cc_start: 0.9080 (mmpt) cc_final: 0.8811 (mmmt) REVERT: V 120 PHE cc_start: 0.9529 (m-80) cc_final: 0.8931 (m-80) REVERT: V 139 ASP cc_start: 0.9328 (m-30) cc_final: 0.9013 (m-30) REVERT: W 2 GLN cc_start: 0.9546 (mt0) cc_final: 0.9286 (pm20) REVERT: W 26 PHE cc_start: 0.9433 (t80) cc_final: 0.9051 (t80) REVERT: W 35 LYS cc_start: 0.9744 (mtpp) cc_final: 0.9513 (mmmm) REVERT: W 52 MET cc_start: 0.9571 (mtp) cc_final: 0.9039 (ttm) REVERT: W 56 GLU cc_start: 0.9488 (tt0) cc_final: 0.9114 (tp30) REVERT: W 60 ASP cc_start: 0.9543 (m-30) cc_final: 0.9248 (m-30) REVERT: W 102 ARG cc_start: 0.8243 (mtt180) cc_final: 0.8018 (mtp85) REVERT: W 108 MET cc_start: 0.9305 (ptt) cc_final: 0.8863 (ppp) REVERT: W 120 PHE cc_start: 0.9510 (m-80) cc_final: 0.9112 (m-80) REVERT: W 131 ILE cc_start: 0.9448 (tt) cc_final: 0.9185 (tp) REVERT: X 23 ASN cc_start: 0.9739 (m-40) cc_final: 0.9503 (m-40) REVERT: X 26 PHE cc_start: 0.9681 (t80) cc_final: 0.9195 (t80) REVERT: X 27 LEU cc_start: 0.9361 (mt) cc_final: 0.8916 (mt) REVERT: X 71 TYR cc_start: 0.9568 (m-80) cc_final: 0.8986 (m-80) REVERT: X 111 LYS cc_start: 0.9214 (mmpt) cc_final: 0.8966 (mmmt) REVERT: X 120 PHE cc_start: 0.9488 (m-80) cc_final: 0.9150 (m-80) outliers start: 6 outliers final: 1 residues processed: 1514 average time/residue: 0.4866 time to fit residues: 1095.8449 Evaluate side-chains 1165 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1164 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 5.9990 chunk 313 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 204 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 348 optimal weight: 0.5980 chunk 289 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 70 ASN B 130 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 129 HIS F 118 ASN F 130 HIS F 156 GLN E 34 HIS E 130 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 HIS G 156 GLN H 34 HIS I 76 HIS I 130 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 HIS ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS Q 34 HIS Q 130 HIS ** R 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 HIS R 130 HIS S 34 HIS S 130 HIS S 156 GLN ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 130 HIS T 156 GLN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 HIS V 156 GLN W 34 HIS ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 HIS X 129 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32072 Z= 0.197 Angle : 0.670 12.913 43500 Z= 0.327 Chirality : 0.039 0.208 4829 Planarity : 0.003 0.054 5615 Dihedral : 7.905 89.711 4222 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.30 % Allowed : 3.46 % Favored : 96.23 % 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: -0.41 (0.13), residues: 3742 helix: 0.30 (0.09), residues: 3032 sheet: None (None), residues: 0 loop : -2.44 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 37 HIS 0.013 0.001 HIS K 34 PHE 0.037 0.002 PHE Q 10 TYR 0.015 0.001 TYR E 71 ARG 0.007 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1561 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1551 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9734 (pt0) cc_final: 0.9457 (tp30) REVERT: A 23 ASN cc_start: 0.9790 (m-40) cc_final: 0.9434 (m-40) REVERT: A 26 PHE cc_start: 0.9654 (t80) cc_final: 0.9110 (t80) REVERT: A 27 LEU cc_start: 0.9246 (mt) cc_final: 0.8848 (mt) REVERT: A 100 ARG cc_start: 0.9535 (mmm160) cc_final: 0.9316 (mmm-85) REVERT: A 102 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7171 (mtt180) REVERT: A 111 LYS cc_start: 0.9095 (mmpt) cc_final: 0.8851 (mmmt) REVERT: A 139 ASP cc_start: 0.9478 (m-30) cc_final: 0.9237 (m-30) REVERT: B 1 MET cc_start: 0.9230 (mpp) cc_final: 0.8679 (tmm) REVERT: B 2 GLN cc_start: 0.9523 (mt0) cc_final: 0.9275 (pm20) REVERT: B 23 ASN cc_start: 0.9586 (m-40) cc_final: 0.9348 (m-40) REVERT: B 26 PHE cc_start: 0.9451 (t80) cc_final: 0.9028 (t80) REVERT: B 35 LYS cc_start: 0.9772 (mtpp) cc_final: 0.9492 (mmmm) REVERT: B 56 GLU cc_start: 0.9507 (tt0) cc_final: 0.9220 (tp30) REVERT: B 86 MET cc_start: 0.9455 (pmm) cc_final: 0.9154 (pmm) REVERT: B 100 ARG cc_start: 0.9424 (mmt180) cc_final: 0.9142 (mmm160) REVERT: B 111 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8781 (mmmt) REVERT: B 127 GLU cc_start: 0.9549 (mm-30) cc_final: 0.9225 (mm-30) REVERT: B 139 ASP cc_start: 0.9509 (m-30) cc_final: 0.9259 (m-30) REVERT: B 154 ILE cc_start: 0.9648 (pt) cc_final: 0.9398 (mm) REVERT: C 23 ASN cc_start: 0.9602 (m-40) cc_final: 0.9174 (t0) REVERT: C 26 PHE cc_start: 0.9676 (t80) cc_final: 0.9238 (t80) REVERT: C 27 LEU cc_start: 0.9454 (mt) cc_final: 0.8869 (mt) REVERT: C 100 ARG cc_start: 0.9429 (mmt180) cc_final: 0.9165 (mmm160) REVERT: C 102 ARG cc_start: 0.8476 (mtt180) cc_final: 0.8153 (mtp85) REVERT: C 111 LYS cc_start: 0.9223 (mmpt) cc_final: 0.8944 (mmmt) REVERT: C 120 PHE cc_start: 0.9457 (m-80) cc_final: 0.8939 (m-80) REVERT: C 130 HIS cc_start: 0.9200 (t-90) cc_final: 0.8907 (t-90) REVERT: C 139 ASP cc_start: 0.9283 (m-30) cc_final: 0.9069 (m-30) REVERT: D 1 MET cc_start: 0.9024 (mmp) cc_final: 0.8435 (tmm) REVERT: D 2 GLN cc_start: 0.9619 (mt0) cc_final: 0.9275 (pm20) REVERT: D 27 LEU cc_start: 0.9323 (mt) cc_final: 0.9008 (mt) REVERT: D 52 MET cc_start: 0.8720 (mtm) cc_final: 0.8217 (ptm) REVERT: D 120 PHE cc_start: 0.9520 (m-80) cc_final: 0.9075 (m-10) REVERT: D 123 ILE cc_start: 0.9256 (tt) cc_final: 0.8995 (tt) REVERT: F 10 PHE cc_start: 0.9574 (m-80) cc_final: 0.9342 (m-80) REVERT: F 23 ASN cc_start: 0.9673 (m-40) cc_final: 0.9246 (t0) REVERT: F 26 PHE cc_start: 0.9591 (t80) cc_final: 0.9277 (t80) REVERT: F 27 LEU cc_start: 0.9318 (mm) cc_final: 0.8355 (mm) REVERT: F 56 GLU cc_start: 0.9587 (tt0) cc_final: 0.9362 (tp30) REVERT: F 60 ASP cc_start: 0.9824 (p0) cc_final: 0.9502 (p0) REVERT: F 61 ARG cc_start: 0.9805 (tpt-90) cc_final: 0.9560 (tpt170) REVERT: F 71 TYR cc_start: 0.9430 (m-10) cc_final: 0.8652 (m-80) REVERT: F 86 MET cc_start: 0.9407 (pmm) cc_final: 0.9116 (pmm) REVERT: F 111 LYS cc_start: 0.9252 (mmmt) cc_final: 0.8872 (mmmt) REVERT: F 129 HIS cc_start: 0.9416 (m90) cc_final: 0.9202 (m90) REVERT: F 130 HIS cc_start: 0.9589 (OUTLIER) cc_final: 0.9228 (t-90) REVERT: F 139 ASP cc_start: 0.9326 (m-30) cc_final: 0.9123 (m-30) REVERT: E 26 PHE cc_start: 0.9609 (t80) cc_final: 0.9112 (t80) REVERT: E 86 MET cc_start: 0.9496 (pmm) cc_final: 0.9235 (pmm) REVERT: E 111 LYS cc_start: 0.9301 (mmmt) cc_final: 0.8970 (mmmt) REVERT: E 120 PHE cc_start: 0.9523 (m-10) cc_final: 0.9300 (m-10) REVERT: E 127 GLU cc_start: 0.9600 (mm-30) cc_final: 0.9308 (pt0) REVERT: E 129 HIS cc_start: 0.9426 (m90) cc_final: 0.9160 (m90) REVERT: E 130 HIS cc_start: 0.8943 (t-90) cc_final: 0.8572 (t-90) REVERT: G 2 GLN cc_start: 0.9560 (mt0) cc_final: 0.9299 (pm20) REVERT: G 9 GLU cc_start: 0.9648 (tp30) cc_final: 0.9445 (pt0) REVERT: G 23 ASN cc_start: 0.9688 (m-40) cc_final: 0.9350 (t0) REVERT: G 27 LEU cc_start: 0.9208 (mt) cc_final: 0.8782 (mt) REVERT: G 52 MET cc_start: 0.9260 (mtm) cc_final: 0.9026 (mtm) REVERT: G 86 MET cc_start: 0.9499 (pmm) cc_final: 0.9258 (pmm) REVERT: G 108 MET cc_start: 0.9620 (mtm) cc_final: 0.9083 (tmm) REVERT: G 120 PHE cc_start: 0.9008 (m-80) cc_final: 0.8793 (m-80) REVERT: G 123 ILE cc_start: 0.9485 (mm) cc_final: 0.9154 (mm) REVERT: G 127 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9055 (mm-30) REVERT: G 139 ASP cc_start: 0.9314 (m-30) cc_final: 0.9032 (m-30) REVERT: G 141 ILE cc_start: 0.9598 (mt) cc_final: 0.9356 (mt) REVERT: H 1 MET cc_start: 0.9393 (mpp) cc_final: 0.9074 (mpp) REVERT: H 23 ASN cc_start: 0.9642 (m-40) cc_final: 0.9301 (t0) REVERT: H 26 PHE cc_start: 0.9609 (t80) cc_final: 0.9193 (t80) REVERT: H 27 LEU cc_start: 0.9230 (mt) cc_final: 0.8718 (mt) REVERT: H 35 LYS cc_start: 0.9799 (mmmm) cc_final: 0.9500 (mmmm) REVERT: H 71 TYR cc_start: 0.9192 (m-80) cc_final: 0.8538 (m-80) REVERT: H 100 ARG cc_start: 0.9129 (mmp80) cc_final: 0.8897 (mmm160) REVERT: H 111 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8799 (mmmt) REVERT: H 139 ASP cc_start: 0.9543 (m-30) cc_final: 0.9336 (m-30) REVERT: I 2 GLN cc_start: 0.9593 (mt0) cc_final: 0.9307 (mm-40) REVERT: I 6 GLU cc_start: 0.9593 (tp30) cc_final: 0.9291 (tp30) REVERT: I 10 PHE cc_start: 0.9583 (m-10) cc_final: 0.9125 (m-80) REVERT: I 23 ASN cc_start: 0.9635 (m-40) cc_final: 0.9148 (t0) REVERT: I 24 GLN cc_start: 0.9526 (tt0) cc_final: 0.9176 (tm-30) REVERT: I 26 PHE cc_start: 0.9620 (t80) cc_final: 0.9119 (t80) REVERT: I 27 LEU cc_start: 0.9316 (mt) cc_final: 0.8620 (mt) REVERT: I 111 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8777 (mmmt) REVERT: I 120 PHE cc_start: 0.9487 (m-80) cc_final: 0.9094 (m-80) REVERT: J 26 PHE cc_start: 0.9621 (t80) cc_final: 0.9417 (t80) REVERT: J 52 MET cc_start: 0.8719 (mtm) cc_final: 0.8321 (mtm) REVERT: J 60 ASP cc_start: 0.9937 (p0) cc_final: 0.9682 (p0) REVERT: J 120 PHE cc_start: 0.9407 (m-80) cc_final: 0.9153 (m-80) REVERT: K 1 MET cc_start: 0.9000 (mpp) cc_final: 0.8739 (tmm) REVERT: K 26 PHE cc_start: 0.9576 (t80) cc_final: 0.9225 (t80) REVERT: K 61 ARG cc_start: 0.9840 (tpt170) cc_final: 0.9620 (tpt170) REVERT: K 71 TYR cc_start: 0.9601 (m-80) cc_final: 0.9306 (m-80) REVERT: K 99 ASP cc_start: 0.9149 (p0) cc_final: 0.8834 (p0) REVERT: K 100 ARG cc_start: 0.9467 (mmt-90) cc_final: 0.9160 (mmm160) REVERT: K 109 ARG cc_start: 0.9467 (mtt-85) cc_final: 0.9131 (ttt-90) REVERT: K 111 LYS cc_start: 0.9141 (mmpt) cc_final: 0.8865 (mmmt) REVERT: K 120 PHE cc_start: 0.9393 (m-80) cc_final: 0.8944 (m-80) REVERT: L 23 ASN cc_start: 0.9574 (m-40) cc_final: 0.9101 (m-40) REVERT: L 26 PHE cc_start: 0.9641 (t80) cc_final: 0.9130 (t80) REVERT: L 27 LEU cc_start: 0.9490 (mt) cc_final: 0.8958 (mm) REVERT: L 34 HIS cc_start: 0.9292 (t70) cc_final: 0.8991 (t-90) REVERT: L 52 MET cc_start: 0.9559 (mtp) cc_final: 0.8615 (mtp) REVERT: L 53 ARG cc_start: 0.9206 (ttp-110) cc_final: 0.8945 (ptp-110) REVERT: L 100 ARG cc_start: 0.9320 (mmp80) cc_final: 0.9065 (mmm160) REVERT: L 111 LYS cc_start: 0.9151 (mmpt) cc_final: 0.8903 (mmmt) REVERT: L 130 HIS cc_start: 0.9084 (t-90) cc_final: 0.8772 (t-90) REVERT: L 131 ILE cc_start: 0.9052 (tt) cc_final: 0.8797 (tt) REVERT: L 139 ASP cc_start: 0.9285 (m-30) cc_final: 0.9067 (m-30) REVERT: M 1 MET cc_start: 0.9037 (mmm) cc_final: 0.8447 (tmm) REVERT: M 2 GLN cc_start: 0.9580 (mt0) cc_final: 0.8952 (pp30) REVERT: M 26 PHE cc_start: 0.9609 (t80) cc_final: 0.9312 (t80) REVERT: M 27 LEU cc_start: 0.9401 (mt) cc_final: 0.9103 (mt) REVERT: M 73 ARG cc_start: 0.9493 (mmp80) cc_final: 0.9268 (mmm160) REVERT: M 101 LEU cc_start: 0.9574 (mt) cc_final: 0.9341 (mt) REVERT: M 111 LYS cc_start: 0.9082 (mmpt) cc_final: 0.8859 (mmmt) REVERT: M 114 ILE cc_start: 0.8754 (mp) cc_final: 0.8544 (mm) REVERT: M 120 PHE cc_start: 0.9466 (m-80) cc_final: 0.9083 (m-10) REVERT: M 130 HIS cc_start: 0.9349 (t-170) cc_final: 0.9018 (t-170) REVERT: M 139 ASP cc_start: 0.9505 (m-30) cc_final: 0.9242 (m-30) REVERT: M 155 GLU cc_start: 0.8922 (tp30) cc_final: 0.8623 (mp0) REVERT: M 156 GLN cc_start: 0.7098 (tt0) cc_final: 0.5686 (tt0) REVERT: N 2 GLN cc_start: 0.9561 (mt0) cc_final: 0.9292 (pm20) REVERT: N 23 ASN cc_start: 0.9557 (m-40) cc_final: 0.9225 (t0) REVERT: N 26 PHE cc_start: 0.9473 (t80) cc_final: 0.9050 (t80) REVERT: N 27 LEU cc_start: 0.9384 (mt) cc_final: 0.8954 (mt) REVERT: N 34 HIS cc_start: 0.8133 (p90) cc_final: 0.7789 (p90) REVERT: N 35 LYS cc_start: 0.9605 (tptp) cc_final: 0.9329 (tppt) REVERT: N 43 TYR cc_start: 0.9675 (t80) cc_final: 0.9341 (t80) REVERT: N 108 MET cc_start: 0.9317 (ptt) cc_final: 0.8526 (ppp) REVERT: N 111 LYS cc_start: 0.9013 (mmpt) cc_final: 0.8765 (mmmt) REVERT: N 120 PHE cc_start: 0.9569 (m-80) cc_final: 0.9313 (m-80) REVERT: N 139 ASP cc_start: 0.9446 (m-30) cc_final: 0.9211 (m-30) REVERT: O 25 TYR cc_start: 0.9532 (m-10) cc_final: 0.9321 (m-10) REVERT: O 26 PHE cc_start: 0.9555 (t80) cc_final: 0.9158 (t80) REVERT: O 27 LEU cc_start: 0.9341 (mp) cc_final: 0.8786 (mp) REVERT: O 32 GLN cc_start: 0.9355 (pt0) cc_final: 0.9093 (pt0) REVERT: O 108 MET cc_start: 0.9532 (mtt) cc_final: 0.9051 (ptp) REVERT: O 120 PHE cc_start: 0.9381 (m-80) cc_final: 0.8885 (m-80) REVERT: P 23 ASN cc_start: 0.9792 (m-40) cc_final: 0.9512 (m-40) REVERT: P 26 PHE cc_start: 0.9414 (t80) cc_final: 0.8868 (t80) REVERT: P 27 LEU cc_start: 0.9349 (mt) cc_final: 0.8940 (mt) REVERT: P 32 GLN cc_start: 0.9572 (pm20) cc_final: 0.9017 (pm20) REVERT: P 111 LYS cc_start: 0.9137 (mmpt) cc_final: 0.8928 (mmmt) REVERT: P 120 PHE cc_start: 0.9426 (m-80) cc_final: 0.8954 (m-80) REVERT: P 130 HIS cc_start: 0.9277 (t70) cc_final: 0.8868 (t70) REVERT: P 139 ASP cc_start: 0.9260 (m-30) cc_final: 0.9029 (m-30) REVERT: Q 1 MET cc_start: 0.9334 (mmp) cc_final: 0.9100 (mmp) REVERT: Q 23 ASN cc_start: 0.9721 (m-40) cc_final: 0.9153 (p0) REVERT: Q 26 PHE cc_start: 0.9626 (t80) cc_final: 0.9132 (t80) REVERT: Q 27 LEU cc_start: 0.9442 (mt) cc_final: 0.9144 (mt) REVERT: Q 43 TYR cc_start: 0.9751 (t80) cc_final: 0.9445 (t80) REVERT: Q 56 GLU cc_start: 0.9525 (tm-30) cc_final: 0.9323 (tp30) REVERT: Q 120 PHE cc_start: 0.9570 (m-10) cc_final: 0.9339 (m-10) REVERT: Q 130 HIS cc_start: 0.9055 (t-90) cc_final: 0.8743 (t-90) REVERT: Q 139 ASP cc_start: 0.9411 (m-30) cc_final: 0.9194 (m-30) REVERT: R 27 LEU cc_start: 0.9594 (tt) cc_final: 0.9239 (mt) REVERT: R 43 TYR cc_start: 0.9546 (t80) cc_final: 0.9176 (t80) REVERT: R 49 PHE cc_start: 0.9687 (m-80) cc_final: 0.9361 (m-80) REVERT: R 52 MET cc_start: 0.9579 (mtm) cc_final: 0.9193 (mtm) REVERT: R 56 GLU cc_start: 0.9367 (tt0) cc_final: 0.9158 (tp30) REVERT: R 108 MET cc_start: 0.9270 (ptt) cc_final: 0.8827 (ppp) REVERT: R 139 ASP cc_start: 0.9488 (m-30) cc_final: 0.9262 (m-30) REVERT: R 155 GLU cc_start: 0.9113 (tp30) cc_final: 0.8453 (tm-30) REVERT: S 23 ASN cc_start: 0.9528 (t0) cc_final: 0.9194 (t0) REVERT: S 27 LEU cc_start: 0.9260 (mt) cc_final: 0.9052 (pp) REVERT: S 45 ARG cc_start: 0.9349 (ttt90) cc_final: 0.8998 (ttm170) REVERT: S 111 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8853 (mmmt) REVERT: S 120 PHE cc_start: 0.9336 (m-80) cc_final: 0.8837 (m-80) REVERT: T 2 GLN cc_start: 0.9535 (mt0) cc_final: 0.9245 (mm-40) REVERT: T 26 PHE cc_start: 0.9636 (t80) cc_final: 0.9402 (t80) REVERT: T 32 GLN cc_start: 0.9749 (mt0) cc_final: 0.9486 (pt0) REVERT: T 86 MET cc_start: 0.9695 (pmm) cc_final: 0.9480 (pmm) REVERT: T 108 MET cc_start: 0.9334 (tpt) cc_final: 0.8745 (tpt) REVERT: T 120 PHE cc_start: 0.9492 (m-10) cc_final: 0.9224 (m-10) REVERT: T 127 GLU cc_start: 0.9557 (mm-30) cc_final: 0.9307 (mm-30) REVERT: T 139 ASP cc_start: 0.9426 (m-30) cc_final: 0.9189 (m-30) REVERT: U 23 ASN cc_start: 0.9573 (m-40) cc_final: 0.8996 (t0) REVERT: U 24 GLN cc_start: 0.9647 (tt0) cc_final: 0.9232 (tp-100) REVERT: U 26 PHE cc_start: 0.9602 (t80) cc_final: 0.8977 (t80) REVERT: U 27 LEU cc_start: 0.9553 (tp) cc_final: 0.9222 (mt) REVERT: U 86 MET cc_start: 0.9829 (ptp) cc_final: 0.9620 (ptp) REVERT: U 108 MET cc_start: 0.9424 (ptt) cc_final: 0.9053 (ppp) REVERT: U 120 PHE cc_start: 0.9380 (m-80) cc_final: 0.9033 (m-80) REVERT: U 139 ASP cc_start: 0.9483 (m-30) cc_final: 0.9241 (m-30) REVERT: V 23 ASN cc_start: 0.9620 (m-40) cc_final: 0.9328 (t0) REVERT: V 26 PHE cc_start: 0.9676 (t80) cc_final: 0.9040 (t80) REVERT: V 27 LEU cc_start: 0.9443 (mt) cc_final: 0.8797 (mt) REVERT: V 108 MET cc_start: 0.9429 (ptt) cc_final: 0.8810 (ppp) REVERT: V 111 LYS cc_start: 0.9074 (mmpt) cc_final: 0.8782 (mmmt) REVERT: V 120 PHE cc_start: 0.9485 (m-80) cc_final: 0.9113 (m-80) REVERT: V 139 ASP cc_start: 0.9319 (m-30) cc_final: 0.8924 (m-30) REVERT: W 2 GLN cc_start: 0.9580 (mt0) cc_final: 0.9359 (pm20) REVERT: W 23 ASN cc_start: 0.9571 (m-40) cc_final: 0.9288 (t0) REVERT: W 26 PHE cc_start: 0.9377 (t80) cc_final: 0.8971 (t80) REVERT: W 52 MET cc_start: 0.9568 (mtp) cc_final: 0.9015 (ttm) REVERT: W 56 GLU cc_start: 0.9481 (tt0) cc_final: 0.9111 (tp30) REVERT: W 60 ASP cc_start: 0.9511 (m-30) cc_final: 0.9208 (m-30) REVERT: W 108 MET cc_start: 0.9282 (ptt) cc_final: 0.8683 (ppp) REVERT: W 109 ARG cc_start: 0.9288 (mtp180) cc_final: 0.8800 (tpm170) REVERT: W 111 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8899 (mmmt) REVERT: W 120 PHE cc_start: 0.9501 (m-80) cc_final: 0.9084 (m-80) REVERT: W 129 HIS cc_start: 0.9221 (m90) cc_final: 0.8951 (m90) REVERT: W 155 GLU cc_start: 0.8852 (tp30) cc_final: 0.8126 (tm-30) REVERT: X 16 THR cc_start: 0.8766 (m) cc_final: 0.8554 (m) REVERT: X 26 PHE cc_start: 0.9650 (t80) cc_final: 0.9120 (t80) REVERT: X 27 LEU cc_start: 0.9317 (mt) cc_final: 0.8946 (mt) REVERT: X 32 GLN cc_start: 0.9570 (pm20) cc_final: 0.9043 (pm20) REVERT: X 111 LYS cc_start: 0.9196 (mmpt) cc_final: 0.8969 (mmmt) REVERT: X 120 PHE cc_start: 0.9520 (m-80) cc_final: 0.9143 (m-10) REVERT: X 139 ASP cc_start: 0.9412 (m-30) cc_final: 0.9174 (m-30) outliers start: 10 outliers final: 1 residues processed: 1554 average time/residue: 0.4917 time to fit residues: 1136.0781 Evaluate side-chains 1195 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1193 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 293 optimal weight: 0.3980 chunk 194 optimal weight: 0.0070 chunk 346 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 overall best weight: 3.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 156 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS F 156 GLN E 34 HIS E 156 GLN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS H 130 HIS I 76 HIS I 129 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 HIS ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS Q 34 HIS Q 156 GLN ** R 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 HIS S 130 HIS S 156 GLN ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS ** T 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 156 GLN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS ** V 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 34 HIS ** X 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 HIS X 130 HIS X 156 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32072 Z= 0.215 Angle : 0.725 22.990 43500 Z= 0.353 Chirality : 0.041 0.236 4829 Planarity : 0.004 0.054 5615 Dihedral : 7.852 89.967 4222 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.15 % Allowed : 2.47 % Favored : 97.38 % 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: -0.48 (0.13), residues: 3742 helix: 0.22 (0.09), residues: 3053 sheet: None (None), residues: 0 loop : -2.38 (0.20), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 37 HIS 0.010 0.001 HIS K 34 PHE 0.059 0.003 PHE S 49 TYR 0.028 0.002 TYR U 133 ARG 0.006 0.001 ARG W 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1529 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1524 time to evaluate : 3.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 23 ASN cc_start: 0.9778 (m-40) cc_final: 0.9419 (m-40) REVERT: A 26 PHE cc_start: 0.9649 (t80) cc_final: 0.9129 (t80) REVERT: A 27 LEU cc_start: 0.9274 (mt) cc_final: 0.8899 (mt) REVERT: A 71 TYR cc_start: 0.8884 (m-10) cc_final: 0.8438 (m-80) REVERT: A 102 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7298 (mtt180) REVERT: A 111 LYS cc_start: 0.9082 (mmpt) cc_final: 0.8838 (mmmt) REVERT: A 120 PHE cc_start: 0.9090 (m-10) cc_final: 0.8833 (m-10) REVERT: A 123 ILE cc_start: 0.8878 (tt) cc_final: 0.8671 (tt) REVERT: A 139 ASP cc_start: 0.9478 (m-30) cc_final: 0.9245 (m-30) REVERT: B 1 MET cc_start: 0.9102 (mpp) cc_final: 0.8676 (tmm) REVERT: B 2 GLN cc_start: 0.9540 (mt0) cc_final: 0.9304 (pm20) REVERT: B 23 ASN cc_start: 0.9588 (m-40) cc_final: 0.9214 (p0) REVERT: B 26 PHE cc_start: 0.9419 (t80) cc_final: 0.9104 (t80) REVERT: B 34 HIS cc_start: 0.9206 (t-90) cc_final: 0.8976 (t-90) REVERT: B 35 LYS cc_start: 0.9752 (mtpp) cc_final: 0.9480 (mmmm) REVERT: B 43 TYR cc_start: 0.9011 (m-80) cc_final: 0.8628 (m-80) REVERT: B 56 GLU cc_start: 0.9489 (tt0) cc_final: 0.9214 (tp30) REVERT: B 86 MET cc_start: 0.9459 (pmm) cc_final: 0.9202 (pmm) REVERT: B 111 LYS cc_start: 0.9037 (mmmt) cc_final: 0.8709 (mmmt) REVERT: B 127 GLU cc_start: 0.9609 (mm-30) cc_final: 0.9297 (mm-30) REVERT: B 129 HIS cc_start: 0.9432 (m90) cc_final: 0.9183 (m90) REVERT: B 139 ASP cc_start: 0.9494 (m-30) cc_final: 0.9241 (m-30) REVERT: B 154 ILE cc_start: 0.9638 (pt) cc_final: 0.9380 (mm) REVERT: C 1 MET cc_start: 0.9465 (mmp) cc_final: 0.9237 (mmp) REVERT: C 23 ASN cc_start: 0.9640 (m-40) cc_final: 0.9026 (p0) REVERT: C 26 PHE cc_start: 0.9689 (t80) cc_final: 0.9370 (t80) REVERT: C 27 LEU cc_start: 0.9498 (mt) cc_final: 0.9089 (mt) REVERT: C 33 ASP cc_start: 0.8962 (p0) cc_final: 0.8718 (p0) REVERT: C 100 ARG cc_start: 0.9422 (mmt180) cc_final: 0.9156 (mmm160) REVERT: C 102 ARG cc_start: 0.8482 (mtt180) cc_final: 0.8142 (mtp85) REVERT: C 111 LYS cc_start: 0.9167 (mmpt) cc_final: 0.8910 (mmmt) REVERT: C 120 PHE cc_start: 0.9510 (m-80) cc_final: 0.9020 (m-80) REVERT: C 130 HIS cc_start: 0.9222 (t-90) cc_final: 0.8840 (t-90) REVERT: D 1 MET cc_start: 0.8985 (mmp) cc_final: 0.8271 (tmm) REVERT: D 2 GLN cc_start: 0.9622 (mt0) cc_final: 0.9411 (pm20) REVERT: D 27 LEU cc_start: 0.9324 (mt) cc_final: 0.8801 (mt) REVERT: D 101 LEU cc_start: 0.9611 (mt) cc_final: 0.9239 (mt) REVERT: D 120 PHE cc_start: 0.9554 (m-80) cc_final: 0.9112 (m-80) REVERT: F 23 ASN cc_start: 0.9663 (m-40) cc_final: 0.9280 (t0) REVERT: F 26 PHE cc_start: 0.9530 (t80) cc_final: 0.9267 (t80) REVERT: F 27 LEU cc_start: 0.9301 (mm) cc_final: 0.8487 (mm) REVERT: F 33 ASP cc_start: 0.9146 (p0) cc_final: 0.8926 (p0) REVERT: F 56 GLU cc_start: 0.9606 (tt0) cc_final: 0.9391 (tp30) REVERT: F 60 ASP cc_start: 0.9822 (p0) cc_final: 0.9499 (p0) REVERT: F 71 TYR cc_start: 0.9420 (m-10) cc_final: 0.8613 (m-80) REVERT: F 111 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8815 (mmmt) REVERT: E 10 PHE cc_start: 0.9604 (m-80) cc_final: 0.9400 (m-80) REVERT: E 26 PHE cc_start: 0.9598 (t80) cc_final: 0.9078 (t80) REVERT: E 111 LYS cc_start: 0.9347 (mmmt) cc_final: 0.9038 (mmmt) REVERT: E 120 PHE cc_start: 0.9485 (m-10) cc_final: 0.9255 (m-10) REVERT: E 129 HIS cc_start: 0.9456 (m90) cc_final: 0.9195 (m90) REVERT: E 130 HIS cc_start: 0.9076 (t-90) cc_final: 0.8701 (t-90) REVERT: G 2 GLN cc_start: 0.9564 (mt0) cc_final: 0.9314 (pm20) REVERT: G 23 ASN cc_start: 0.9690 (m-40) cc_final: 0.9440 (m-40) REVERT: G 27 LEU cc_start: 0.9218 (mt) cc_final: 0.8867 (mt) REVERT: G 71 TYR cc_start: 0.9423 (m-80) cc_final: 0.8888 (m-80) REVERT: G 86 MET cc_start: 0.9539 (pmm) cc_final: 0.9318 (pmm) REVERT: G 123 ILE cc_start: 0.9462 (mm) cc_final: 0.9116 (mm) REVERT: G 127 GLU cc_start: 0.9339 (mm-30) cc_final: 0.9056 (mm-30) REVERT: H 1 MET cc_start: 0.9453 (mpp) cc_final: 0.9202 (mpp) REVERT: H 23 ASN cc_start: 0.9629 (m-40) cc_final: 0.9308 (t0) REVERT: H 26 PHE cc_start: 0.9601 (t80) cc_final: 0.9169 (t80) REVERT: H 35 LYS cc_start: 0.9771 (mmmm) cc_final: 0.9461 (mmmm) REVERT: H 71 TYR cc_start: 0.9188 (m-80) cc_final: 0.8567 (m-80) REVERT: H 111 LYS cc_start: 0.9103 (mmmt) cc_final: 0.8804 (mmmt) REVERT: H 139 ASP cc_start: 0.9528 (m-30) cc_final: 0.9315 (m-30) REVERT: I 2 GLN cc_start: 0.9580 (mt0) cc_final: 0.9355 (mm-40) REVERT: I 6 GLU cc_start: 0.9618 (tp30) cc_final: 0.9367 (tp30) REVERT: I 9 GLU cc_start: 0.9649 (tp30) cc_final: 0.9434 (tp30) REVERT: I 23 ASN cc_start: 0.9515 (m-40) cc_final: 0.9126 (m-40) REVERT: I 24 GLN cc_start: 0.9485 (tt0) cc_final: 0.9166 (tm-30) REVERT: I 26 PHE cc_start: 0.9651 (t80) cc_final: 0.9313 (t80) REVERT: I 27 LEU cc_start: 0.9322 (mt) cc_final: 0.8861 (mt) REVERT: I 111 LYS cc_start: 0.9000 (mmpt) cc_final: 0.8754 (mmmt) REVERT: I 120 PHE cc_start: 0.9487 (m-80) cc_final: 0.9051 (m-80) REVERT: J 26 PHE cc_start: 0.9620 (t80) cc_final: 0.9420 (t80) REVERT: J 52 MET cc_start: 0.8948 (mtm) cc_final: 0.8659 (mtt) REVERT: J 86 MET cc_start: 0.9542 (pmm) cc_final: 0.9319 (pmm) REVERT: J 120 PHE cc_start: 0.9410 (m-80) cc_final: 0.9162 (m-80) REVERT: K 26 PHE cc_start: 0.9503 (t80) cc_final: 0.9218 (t80) REVERT: K 71 TYR cc_start: 0.9616 (m-80) cc_final: 0.9284 (m-80) REVERT: K 99 ASP cc_start: 0.9049 (p0) cc_final: 0.8744 (p0) REVERT: K 100 ARG cc_start: 0.9472 (mmt-90) cc_final: 0.9165 (mmm160) REVERT: K 108 MET cc_start: 0.9421 (ptt) cc_final: 0.8624 (ppp) REVERT: K 111 LYS cc_start: 0.9086 (mmpt) cc_final: 0.8799 (mmmt) REVERT: K 120 PHE cc_start: 0.9422 (m-80) cc_final: 0.9065 (m-80) REVERT: K 156 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8236 (tm-30) REVERT: L 1 MET cc_start: 0.9431 (mmp) cc_final: 0.9178 (mmp) REVERT: L 26 PHE cc_start: 0.9622 (t80) cc_final: 0.9164 (t80) REVERT: L 27 LEU cc_start: 0.9507 (mt) cc_final: 0.9040 (mt) REVERT: L 34 HIS cc_start: 0.9299 (t70) cc_final: 0.9013 (t-90) REVERT: L 52 MET cc_start: 0.9575 (mtp) cc_final: 0.8677 (mtp) REVERT: L 53 ARG cc_start: 0.9226 (ttp-110) cc_final: 0.9006 (ptp-110) REVERT: L 61 ARG cc_start: 0.9730 (tpt170) cc_final: 0.9527 (ttt180) REVERT: L 109 ARG cc_start: 0.9729 (mtp-110) cc_final: 0.9420 (ptp-110) REVERT: L 111 LYS cc_start: 0.9087 (mmpt) cc_final: 0.8853 (mmmt) REVERT: L 130 HIS cc_start: 0.9086 (t-90) cc_final: 0.8783 (t-90) REVERT: M 1 MET cc_start: 0.9059 (mmm) cc_final: 0.8417 (tmm) REVERT: M 2 GLN cc_start: 0.9587 (mt0) cc_final: 0.9013 (pp30) REVERT: M 26 PHE cc_start: 0.9595 (t80) cc_final: 0.9315 (t80) REVERT: M 27 LEU cc_start: 0.9425 (mt) cc_final: 0.9131 (mt) REVERT: M 52 MET cc_start: 0.8716 (mtm) cc_final: 0.8441 (mtm) REVERT: M 101 LEU cc_start: 0.9569 (mt) cc_final: 0.9334 (mt) REVERT: M 111 LYS cc_start: 0.9020 (mmpt) cc_final: 0.8807 (mmmt) REVERT: M 120 PHE cc_start: 0.9478 (m-80) cc_final: 0.9067 (m-10) REVERT: M 130 HIS cc_start: 0.9394 (t-170) cc_final: 0.9093 (t-170) REVERT: M 139 ASP cc_start: 0.9497 (m-30) cc_final: 0.9237 (m-30) REVERT: M 155 GLU cc_start: 0.9012 (tp30) cc_final: 0.8674 (mp0) REVERT: M 156 GLN cc_start: 0.7427 (tt0) cc_final: 0.5600 (tt0) REVERT: N 2 GLN cc_start: 0.9652 (mt0) cc_final: 0.9418 (pm20) REVERT: N 23 ASN cc_start: 0.9462 (m-40) cc_final: 0.9040 (t0) REVERT: N 26 PHE cc_start: 0.9462 (t80) cc_final: 0.9030 (t80) REVERT: N 27 LEU cc_start: 0.9365 (mt) cc_final: 0.8812 (mt) REVERT: N 34 HIS cc_start: 0.8147 (p90) cc_final: 0.7777 (p90) REVERT: N 35 LYS cc_start: 0.9661 (tptp) cc_final: 0.9380 (tppt) REVERT: N 108 MET cc_start: 0.9295 (ptt) cc_final: 0.8463 (ppp) REVERT: N 111 LYS cc_start: 0.8969 (mmpt) cc_final: 0.8715 (mmmt) REVERT: N 120 PHE cc_start: 0.9634 (m-80) cc_final: 0.9371 (m-80) REVERT: N 129 HIS cc_start: 0.9609 (m-70) cc_final: 0.9372 (m-70) REVERT: N 139 ASP cc_start: 0.9378 (m-30) cc_final: 0.9123 (m-30) REVERT: N 156 GLN cc_start: 0.7846 (tm-30) cc_final: 0.6745 (tm-30) REVERT: O 26 PHE cc_start: 0.9573 (t80) cc_final: 0.9190 (t80) REVERT: O 27 LEU cc_start: 0.9393 (mp) cc_final: 0.9025 (mp) REVERT: O 32 GLN cc_start: 0.9356 (pt0) cc_final: 0.9117 (pt0) REVERT: O 102 ARG cc_start: 0.8425 (mtt180) cc_final: 0.7753 (mtp180) REVERT: O 108 MET cc_start: 0.9559 (mtt) cc_final: 0.9115 (ptp) REVERT: O 120 PHE cc_start: 0.9345 (m-80) cc_final: 0.8940 (m-80) REVERT: P 23 ASN cc_start: 0.9787 (m-40) cc_final: 0.9507 (m-40) REVERT: P 26 PHE cc_start: 0.9373 (t80) cc_final: 0.8805 (t80) REVERT: P 27 LEU cc_start: 0.9349 (mt) cc_final: 0.8868 (mt) REVERT: P 32 GLN cc_start: 0.9612 (pm20) cc_final: 0.9170 (pm20) REVERT: P 73 ARG cc_start: 0.7243 (ptm-80) cc_final: 0.6891 (tmm160) REVERT: P 78 ARG cc_start: 0.9258 (mpt180) cc_final: 0.9022 (mpt180) REVERT: P 111 LYS cc_start: 0.9114 (mmpt) cc_final: 0.8909 (mmmt) REVERT: P 114 ILE cc_start: 0.9008 (mp) cc_final: 0.8686 (mp) REVERT: P 118 ASN cc_start: 0.9269 (t0) cc_final: 0.9009 (m110) REVERT: P 120 PHE cc_start: 0.9498 (m-80) cc_final: 0.9225 (m-80) REVERT: P 130 HIS cc_start: 0.9386 (t70) cc_final: 0.8981 (t70) REVERT: P 139 ASP cc_start: 0.9258 (m-30) cc_final: 0.9026 (m-30) REVERT: Q 1 MET cc_start: 0.9379 (mmp) cc_final: 0.9071 (mmp) REVERT: Q 23 ASN cc_start: 0.9702 (m-40) cc_final: 0.8896 (p0) REVERT: Q 26 PHE cc_start: 0.9626 (t80) cc_final: 0.9242 (t80) REVERT: Q 27 LEU cc_start: 0.9448 (mt) cc_final: 0.9120 (mp) REVERT: Q 43 TYR cc_start: 0.9759 (t80) cc_final: 0.9448 (t80) REVERT: Q 56 GLU cc_start: 0.9527 (tm-30) cc_final: 0.9324 (tp30) REVERT: Q 120 PHE cc_start: 0.9587 (m-10) cc_final: 0.9345 (m-10) REVERT: Q 130 HIS cc_start: 0.9183 (t-90) cc_final: 0.8887 (t-170) REVERT: Q 139 ASP cc_start: 0.9395 (m-30) cc_final: 0.9194 (m-30) REVERT: R 27 LEU cc_start: 0.9612 (tt) cc_final: 0.9287 (mt) REVERT: R 49 PHE cc_start: 0.9668 (m-80) cc_final: 0.9453 (m-80) REVERT: R 139 ASP cc_start: 0.9484 (m-30) cc_final: 0.9241 (m-30) REVERT: R 155 GLU cc_start: 0.9118 (tp30) cc_final: 0.8456 (tm-30) REVERT: S 27 LEU cc_start: 0.9283 (mt) cc_final: 0.8996 (mt) REVERT: S 45 ARG cc_start: 0.9328 (ttt90) cc_final: 0.9016 (tpp80) REVERT: S 100 ARG cc_start: 0.9301 (mmm160) cc_final: 0.8910 (mmm160) REVERT: S 111 LYS cc_start: 0.9174 (mmmt) cc_final: 0.8812 (mmmt) REVERT: S 120 PHE cc_start: 0.9304 (m-80) cc_final: 0.8660 (m-80) REVERT: T 2 GLN cc_start: 0.9530 (mt0) cc_final: 0.9227 (mm-40) REVERT: T 26 PHE cc_start: 0.9643 (t80) cc_final: 0.9324 (t80) REVERT: T 32 GLN cc_start: 0.9664 (mt0) cc_final: 0.9430 (pt0) REVERT: T 100 ARG cc_start: 0.9462 (mmm160) cc_final: 0.9250 (mmm-85) REVERT: T 108 MET cc_start: 0.9356 (tpt) cc_final: 0.8809 (tpt) REVERT: T 120 PHE cc_start: 0.9520 (m-10) cc_final: 0.9137 (m-10) REVERT: T 123 ILE cc_start: 0.9592 (pt) cc_final: 0.8966 (mm) REVERT: T 126 ASP cc_start: 0.9635 (m-30) cc_final: 0.9423 (m-30) REVERT: T 127 GLU cc_start: 0.9611 (mm-30) cc_final: 0.9147 (mm-30) REVERT: T 130 HIS cc_start: 0.9538 (t70) cc_final: 0.9321 (t70) REVERT: T 139 ASP cc_start: 0.9439 (m-30) cc_final: 0.9216 (m-30) REVERT: U 23 ASN cc_start: 0.9572 (m-40) cc_final: 0.9068 (t0) REVERT: U 24 GLN cc_start: 0.9659 (tt0) cc_final: 0.9240 (tp-100) REVERT: U 26 PHE cc_start: 0.9595 (t80) cc_final: 0.8949 (t80) REVERT: U 27 LEU cc_start: 0.9568 (tp) cc_final: 0.9004 (mt) REVERT: U 86 MET cc_start: 0.9829 (ptp) cc_final: 0.9622 (ptp) REVERT: U 120 PHE cc_start: 0.9464 (m-80) cc_final: 0.9091 (m-80) REVERT: U 139 ASP cc_start: 0.9480 (m-30) cc_final: 0.9244 (m-30) REVERT: V 1 MET cc_start: 0.9464 (mmp) cc_final: 0.9080 (mmp) REVERT: V 23 ASN cc_start: 0.9657 (m-40) cc_final: 0.9313 (t0) REVERT: V 26 PHE cc_start: 0.9651 (t80) cc_final: 0.9011 (t80) REVERT: V 27 LEU cc_start: 0.9441 (mt) cc_final: 0.8778 (mt) REVERT: V 108 MET cc_start: 0.9387 (ptt) cc_final: 0.8824 (ppp) REVERT: V 109 ARG cc_start: 0.9531 (mtp-110) cc_final: 0.9207 (mtp180) REVERT: V 111 LYS cc_start: 0.9031 (mmpt) cc_final: 0.8802 (mmmt) REVERT: V 120 PHE cc_start: 0.9581 (m-80) cc_final: 0.9096 (m-10) REVERT: V 139 ASP cc_start: 0.9330 (m-30) cc_final: 0.9125 (m-30) REVERT: W 2 GLN cc_start: 0.9581 (mt0) cc_final: 0.9376 (pm20) REVERT: W 23 ASN cc_start: 0.9561 (m-40) cc_final: 0.9182 (t0) REVERT: W 26 PHE cc_start: 0.9410 (t80) cc_final: 0.9074 (t80) REVERT: W 52 MET cc_start: 0.9600 (mtp) cc_final: 0.9015 (ttm) REVERT: W 56 GLU cc_start: 0.9480 (tt0) cc_final: 0.9111 (tp30) REVERT: W 60 ASP cc_start: 0.9404 (m-30) cc_final: 0.9132 (m-30) REVERT: W 102 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7916 (mtp85) REVERT: W 111 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8931 (mmmt) REVERT: W 120 PHE cc_start: 0.9524 (m-80) cc_final: 0.8946 (m-80) REVERT: X 16 THR cc_start: 0.8788 (m) cc_final: 0.8562 (m) REVERT: X 23 ASN cc_start: 0.9719 (m-40) cc_final: 0.9512 (m-40) REVERT: X 26 PHE cc_start: 0.9638 (t80) cc_final: 0.9151 (t80) REVERT: X 27 LEU cc_start: 0.9348 (mt) cc_final: 0.8935 (mt) REVERT: X 102 ARG cc_start: 0.7926 (ptp-110) cc_final: 0.7505 (mtt180) REVERT: X 111 LYS cc_start: 0.9193 (mmpt) cc_final: 0.8991 (mmmt) REVERT: X 120 PHE cc_start: 0.9480 (m-80) cc_final: 0.9103 (m-10) REVERT: X 139 ASP cc_start: 0.9368 (m-30) cc_final: 0.9151 (m-30) outliers start: 5 outliers final: 1 residues processed: 1525 average time/residue: 0.5175 time to fit residues: 1181.1157 Evaluate side-chains 1186 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1185 time to evaluate : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 130 HIS B 156 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 118 ASN F 129 HIS F 156 GLN E 34 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS I 76 HIS I 129 HIS I 130 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 HIS ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN M 118 ASN ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS P 28 HIS Q 34 HIS ** Q 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS S 23 ASN S 34 HIS S 130 HIS S 156 GLN ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS ** T 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 156 GLN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 HIS ** V 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 34 HIS W 130 HIS X 34 HIS X 129 HIS X 156 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.6767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 32072 Z= 0.290 Angle : 0.801 23.711 43500 Z= 0.393 Chirality : 0.042 0.205 4829 Planarity : 0.004 0.056 5615 Dihedral : 8.131 88.977 4222 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.30 % Allowed : 2.08 % Favored : 97.62 % 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: -0.35 (0.13), residues: 3742 helix: 0.18 (0.09), residues: 2908 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 37 HIS 0.013 0.002 HIS K 34 PHE 0.047 0.003 PHE E 10 TYR 0.023 0.002 TYR C 149 ARG 0.008 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1458 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9733 (pt0) cc_final: 0.9502 (tp30) REVERT: A 23 ASN cc_start: 0.9804 (m-40) cc_final: 0.9523 (m-40) REVERT: A 26 PHE cc_start: 0.9641 (t80) cc_final: 0.9227 (t80) REVERT: A 102 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7188 (mtt180) REVERT: A 120 PHE cc_start: 0.9111 (m-10) cc_final: 0.8885 (m-10) REVERT: A 139 ASP cc_start: 0.9484 (m-30) cc_final: 0.9249 (m-30) REVERT: B 2 GLN cc_start: 0.9542 (mt0) cc_final: 0.9322 (pm20) REVERT: B 23 ASN cc_start: 0.9514 (m-40) cc_final: 0.9084 (p0) REVERT: B 26 PHE cc_start: 0.9447 (t80) cc_final: 0.9011 (t80) REVERT: B 27 LEU cc_start: 0.9091 (mt) cc_final: 0.8746 (mt) REVERT: B 34 HIS cc_start: 0.9196 (t-90) cc_final: 0.8957 (t-90) REVERT: B 35 LYS cc_start: 0.9753 (mtpp) cc_final: 0.9506 (mmmm) REVERT: B 43 TYR cc_start: 0.8920 (m-80) cc_final: 0.8539 (m-80) REVERT: B 56 GLU cc_start: 0.9511 (tt0) cc_final: 0.9268 (tp30) REVERT: B 86 MET cc_start: 0.9518 (pmm) cc_final: 0.9264 (pmm) REVERT: B 99 ASP cc_start: 0.9417 (p0) cc_final: 0.8997 (p0) REVERT: B 100 ARG cc_start: 0.9416 (mmt180) cc_final: 0.9148 (mmm160) REVERT: B 118 ASN cc_start: 0.9471 (t0) cc_final: 0.9154 (m110) REVERT: B 120 PHE cc_start: 0.9561 (m-80) cc_final: 0.9289 (m-80) REVERT: B 127 GLU cc_start: 0.9604 (mm-30) cc_final: 0.9279 (mm-30) REVERT: B 129 HIS cc_start: 0.9516 (m90) cc_final: 0.9272 (m90) REVERT: B 139 ASP cc_start: 0.9528 (m-30) cc_final: 0.9288 (m-30) REVERT: B 154 ILE cc_start: 0.9607 (pt) cc_final: 0.9334 (mm) REVERT: C 26 PHE cc_start: 0.9665 (t80) cc_final: 0.9184 (t80) REVERT: C 27 LEU cc_start: 0.9493 (mt) cc_final: 0.9013 (mt) REVERT: C 33 ASP cc_start: 0.8984 (p0) cc_final: 0.8738 (p0) REVERT: C 100 ARG cc_start: 0.9457 (mmt180) cc_final: 0.9179 (mmm160) REVERT: C 108 MET cc_start: 0.9585 (ptt) cc_final: 0.8854 (ppp) REVERT: C 111 LYS cc_start: 0.9132 (mmpt) cc_final: 0.8867 (mmmt) REVERT: C 120 PHE cc_start: 0.9547 (m-80) cc_final: 0.9145 (m-10) REVERT: C 130 HIS cc_start: 0.9205 (t-90) cc_final: 0.8826 (t-90) REVERT: D 1 MET cc_start: 0.9089 (mmp) cc_final: 0.8263 (tmm) REVERT: D 2 GLN cc_start: 0.9634 (mt0) cc_final: 0.9389 (pm20) REVERT: D 26 PHE cc_start: 0.9603 (t80) cc_final: 0.9393 (t80) REVERT: D 27 LEU cc_start: 0.9368 (mt) cc_final: 0.8820 (mt) REVERT: D 56 GLU cc_start: 0.9373 (tt0) cc_final: 0.9163 (mm-30) REVERT: D 101 LEU cc_start: 0.9587 (mt) cc_final: 0.9246 (mt) REVERT: D 120 PHE cc_start: 0.9569 (m-80) cc_final: 0.9062 (m-80) REVERT: D 123 ILE cc_start: 0.9443 (tt) cc_final: 0.9240 (tt) REVERT: F 23 ASN cc_start: 0.9666 (m-40) cc_final: 0.9226 (t0) REVERT: F 26 PHE cc_start: 0.9569 (t80) cc_final: 0.9284 (t80) REVERT: F 27 LEU cc_start: 0.9353 (mm) cc_final: 0.8434 (mm) REVERT: F 60 ASP cc_start: 0.9851 (p0) cc_final: 0.9574 (p0) REVERT: F 71 TYR cc_start: 0.9428 (m-10) cc_final: 0.8553 (m-80) REVERT: F 111 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8760 (mmmt) REVERT: F 120 PHE cc_start: 0.9314 (m-80) cc_final: 0.8995 (m-80) REVERT: E 26 PHE cc_start: 0.9600 (t80) cc_final: 0.9103 (t80) REVERT: E 27 LEU cc_start: 0.9202 (mt) cc_final: 0.8847 (mt) REVERT: E 35 LYS cc_start: 0.9783 (mmtt) cc_final: 0.9575 (mmmm) REVERT: E 98 ILE cc_start: 0.8884 (mm) cc_final: 0.8593 (mm) REVERT: E 120 PHE cc_start: 0.9445 (m-10) cc_final: 0.9196 (m-10) REVERT: E 129 HIS cc_start: 0.9486 (m90) cc_final: 0.9236 (m90) REVERT: G 2 GLN cc_start: 0.9557 (mt0) cc_final: 0.9328 (pm20) REVERT: G 23 ASN cc_start: 0.9682 (m-40) cc_final: 0.9435 (m-40) REVERT: G 26 PHE cc_start: 0.9538 (t80) cc_final: 0.9232 (t80) REVERT: G 71 TYR cc_start: 0.9396 (m-80) cc_final: 0.8915 (m-80) REVERT: G 108 MET cc_start: 0.9617 (mtt) cc_final: 0.9389 (ptm) REVERT: G 123 ILE cc_start: 0.9485 (mm) cc_final: 0.9162 (mm) REVERT: G 127 GLU cc_start: 0.9286 (mm-30) cc_final: 0.9044 (mm-30) REVERT: H 1 MET cc_start: 0.9430 (mpp) cc_final: 0.9177 (mpp) REVERT: H 26 PHE cc_start: 0.9615 (t80) cc_final: 0.9167 (t80) REVERT: H 27 LEU cc_start: 0.9217 (mt) cc_final: 0.8728 (mt) REVERT: H 111 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8857 (mmmt) REVERT: H 139 ASP cc_start: 0.9546 (m-30) cc_final: 0.9340 (m-30) REVERT: I 2 GLN cc_start: 0.9603 (mt0) cc_final: 0.9371 (mm-40) REVERT: I 6 GLU cc_start: 0.9640 (tp30) cc_final: 0.9321 (tp30) REVERT: I 10 PHE cc_start: 0.9620 (m-10) cc_final: 0.9152 (m-80) REVERT: I 24 GLN cc_start: 0.9495 (tt0) cc_final: 0.9166 (tm-30) REVERT: I 26 PHE cc_start: 0.9652 (t80) cc_final: 0.9251 (t80) REVERT: I 27 LEU cc_start: 0.9389 (mt) cc_final: 0.9155 (mt) REVERT: I 108 MET cc_start: 0.9739 (ptp) cc_final: 0.9416 (ptp) REVERT: I 111 LYS cc_start: 0.9016 (mmpt) cc_final: 0.8769 (mmmt) REVERT: I 120 PHE cc_start: 0.9555 (m-80) cc_final: 0.9040 (m-80) REVERT: J 26 PHE cc_start: 0.9634 (t80) cc_final: 0.9364 (t80) REVERT: J 27 LEU cc_start: 0.9345 (mt) cc_final: 0.9117 (mt) REVERT: J 52 MET cc_start: 0.9111 (mtm) cc_final: 0.8711 (mtt) REVERT: J 86 MET cc_start: 0.9572 (pmm) cc_final: 0.9327 (pmm) REVERT: J 111 LYS cc_start: 0.9154 (mmpt) cc_final: 0.8926 (mmmt) REVERT: J 120 PHE cc_start: 0.9454 (m-80) cc_final: 0.9180 (m-80) REVERT: K 26 PHE cc_start: 0.9504 (t80) cc_final: 0.9215 (t80) REVERT: K 71 TYR cc_start: 0.9616 (m-80) cc_final: 0.9241 (m-80) REVERT: K 73 ARG cc_start: 0.8152 (ptm-80) cc_final: 0.7790 (tmm160) REVERT: K 111 LYS cc_start: 0.9007 (mmpt) cc_final: 0.8740 (mmmt) REVERT: K 120 PHE cc_start: 0.9498 (m-80) cc_final: 0.9054 (m-80) REVERT: L 1 MET cc_start: 0.9422 (mmp) cc_final: 0.9138 (mmp) REVERT: L 26 PHE cc_start: 0.9618 (t80) cc_final: 0.9139 (t80) REVERT: L 27 LEU cc_start: 0.9531 (mt) cc_final: 0.9113 (mt) REVERT: L 34 HIS cc_start: 0.9341 (t70) cc_final: 0.9063 (t-90) REVERT: L 52 MET cc_start: 0.9567 (mtp) cc_final: 0.8628 (mtp) REVERT: L 53 ARG cc_start: 0.9242 (ttp-110) cc_final: 0.8988 (ptp-110) REVERT: L 109 ARG cc_start: 0.9731 (mtp-110) cc_final: 0.9492 (ptp-110) REVERT: L 114 ILE cc_start: 0.9289 (mp) cc_final: 0.9038 (mp) REVERT: L 118 ASN cc_start: 0.9431 (t0) cc_final: 0.9211 (m110) REVERT: L 130 HIS cc_start: 0.9216 (t-90) cc_final: 0.8800 (t-90) REVERT: M 1 MET cc_start: 0.9098 (mmm) cc_final: 0.8344 (tmm) REVERT: M 2 GLN cc_start: 0.9550 (mt0) cc_final: 0.8956 (pp30) REVERT: M 26 PHE cc_start: 0.9633 (t80) cc_final: 0.9336 (t80) REVERT: M 27 LEU cc_start: 0.9501 (mt) cc_final: 0.9044 (mt) REVERT: M 101 LEU cc_start: 0.9560 (mt) cc_final: 0.9358 (mt) REVERT: M 111 LYS cc_start: 0.9039 (mmpt) cc_final: 0.8817 (mmmt) REVERT: M 120 PHE cc_start: 0.9478 (m-80) cc_final: 0.9070 (m-10) REVERT: M 130 HIS cc_start: 0.9362 (t-170) cc_final: 0.9086 (t-170) REVERT: M 155 GLU cc_start: 0.9070 (tp30) cc_final: 0.8700 (mp0) REVERT: M 156 GLN cc_start: 0.6968 (tt0) cc_final: 0.5455 (tt0) REVERT: N 2 GLN cc_start: 0.9564 (mt0) cc_final: 0.9298 (pm20) REVERT: N 26 PHE cc_start: 0.9471 (t80) cc_final: 0.8999 (t80) REVERT: N 27 LEU cc_start: 0.9416 (mt) cc_final: 0.9000 (mt) REVERT: N 34 HIS cc_start: 0.8225 (p90) cc_final: 0.7829 (p90) REVERT: N 108 MET cc_start: 0.9322 (ptt) cc_final: 0.8516 (ppp) REVERT: N 120 PHE cc_start: 0.9636 (m-80) cc_final: 0.9339 (m-80) REVERT: N 139 ASP cc_start: 0.9394 (m-30) cc_final: 0.9000 (m-30) REVERT: O 26 PHE cc_start: 0.9572 (t80) cc_final: 0.9190 (t80) REVERT: O 27 LEU cc_start: 0.9382 (mp) cc_final: 0.8971 (mp) REVERT: O 32 GLN cc_start: 0.9415 (pt0) cc_final: 0.9151 (pt0) REVERT: O 108 MET cc_start: 0.9561 (mtt) cc_final: 0.9160 (ptm) REVERT: O 120 PHE cc_start: 0.9409 (m-80) cc_final: 0.9092 (m-80) REVERT: O 153 VAL cc_start: 0.9737 (m) cc_final: 0.9456 (p) REVERT: O 156 GLN cc_start: 0.7339 (pp30) cc_final: 0.5992 (pp30) REVERT: P 9 GLU cc_start: 0.9778 (pt0) cc_final: 0.9571 (tp30) REVERT: P 23 ASN cc_start: 0.9802 (m-40) cc_final: 0.9522 (m-40) REVERT: P 26 PHE cc_start: 0.9418 (t80) cc_final: 0.8963 (t80) REVERT: P 27 LEU cc_start: 0.9431 (mt) cc_final: 0.9006 (mt) REVERT: P 43 TYR cc_start: 0.9579 (t80) cc_final: 0.9104 (t80) REVERT: P 100 ARG cc_start: 0.9334 (mmp80) cc_final: 0.9063 (mmm160) REVERT: P 108 MET cc_start: 0.9477 (ptt) cc_final: 0.8780 (ppp) REVERT: P 111 LYS cc_start: 0.9036 (mmpt) cc_final: 0.8819 (mmmt) REVERT: P 114 ILE cc_start: 0.9042 (mp) cc_final: 0.8635 (mp) REVERT: P 118 ASN cc_start: 0.9318 (t0) cc_final: 0.9060 (m110) REVERT: P 120 PHE cc_start: 0.9520 (m-80) cc_final: 0.9144 (m-10) REVERT: P 139 ASP cc_start: 0.9295 (m-30) cc_final: 0.9070 (m-30) REVERT: Q 1 MET cc_start: 0.9379 (mmp) cc_final: 0.9050 (mmp) REVERT: Q 23 ASN cc_start: 0.9697 (m-40) cc_final: 0.9002 (m-40) REVERT: Q 26 PHE cc_start: 0.9612 (t80) cc_final: 0.9133 (t80) REVERT: Q 27 LEU cc_start: 0.9488 (mt) cc_final: 0.8764 (mp) REVERT: Q 100 ARG cc_start: 0.9551 (mmm-85) cc_final: 0.9206 (mmm160) REVERT: Q 120 PHE cc_start: 0.9579 (m-10) cc_final: 0.9357 (m-10) REVERT: Q 130 HIS cc_start: 0.9185 (t-90) cc_final: 0.8719 (t-170) REVERT: R 27 LEU cc_start: 0.9642 (tt) cc_final: 0.9263 (mt) REVERT: R 52 MET cc_start: 0.9243 (mtp) cc_final: 0.8376 (ttm) REVERT: R 114 ILE cc_start: 0.9048 (mm) cc_final: 0.8821 (mm) REVERT: R 118 ASN cc_start: 0.9496 (t0) cc_final: 0.9190 (m-40) REVERT: R 120 PHE cc_start: 0.9500 (m-80) cc_final: 0.9113 (m-80) REVERT: R 155 GLU cc_start: 0.9104 (tp30) cc_final: 0.8460 (tm-30) REVERT: S 27 LEU cc_start: 0.9291 (mt) cc_final: 0.8905 (mt) REVERT: S 56 GLU cc_start: 0.9684 (tt0) cc_final: 0.9431 (tp30) REVERT: S 71 TYR cc_start: 0.9406 (m-80) cc_final: 0.8810 (m-80) REVERT: S 99 ASP cc_start: 0.9156 (p0) cc_final: 0.8726 (p0) REVERT: S 100 ARG cc_start: 0.9378 (mmm160) cc_final: 0.8969 (mmm160) REVERT: S 120 PHE cc_start: 0.9354 (m-80) cc_final: 0.8845 (m-80) REVERT: T 27 LEU cc_start: 0.9254 (mt) cc_final: 0.8826 (mp) REVERT: T 33 ASP cc_start: 0.9149 (t70) cc_final: 0.8620 (m-30) REVERT: T 108 MET cc_start: 0.9325 (tpt) cc_final: 0.8748 (tpt) REVERT: T 120 PHE cc_start: 0.9505 (m-10) cc_final: 0.9227 (m-10) REVERT: T 127 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9302 (mm-30) REVERT: T 130 HIS cc_start: 0.9538 (t70) cc_final: 0.9254 (t70) REVERT: T 139 ASP cc_start: 0.9426 (m-30) cc_final: 0.9180 (m-30) REVERT: U 24 GLN cc_start: 0.9647 (tt0) cc_final: 0.9347 (tp-100) REVERT: U 26 PHE cc_start: 0.9586 (t80) cc_final: 0.8891 (t80) REVERT: U 27 LEU cc_start: 0.9577 (tp) cc_final: 0.9061 (mt) REVERT: U 120 PHE cc_start: 0.9531 (m-80) cc_final: 0.9168 (m-80) REVERT: U 139 ASP cc_start: 0.9512 (m-30) cc_final: 0.9299 (m-30) REVERT: V 23 ASN cc_start: 0.9644 (m-40) cc_final: 0.9337 (m-40) REVERT: V 26 PHE cc_start: 0.9662 (t80) cc_final: 0.9085 (t80) REVERT: V 27 LEU cc_start: 0.9464 (mt) cc_final: 0.8855 (mt) REVERT: V 72 GLN cc_start: 0.9569 (pm20) cc_final: 0.9332 (pm20) REVERT: V 108 MET cc_start: 0.9452 (ptt) cc_final: 0.8845 (ppp) REVERT: V 111 LYS cc_start: 0.9067 (mmpt) cc_final: 0.8788 (mmmt) REVERT: V 120 PHE cc_start: 0.9604 (m-80) cc_final: 0.9192 (m-10) REVERT: V 139 ASP cc_start: 0.9344 (m-30) cc_final: 0.9124 (m-30) REVERT: W 1 MET cc_start: 0.9190 (mpp) cc_final: 0.8913 (mpp) REVERT: W 2 GLN cc_start: 0.9599 (mt0) cc_final: 0.9396 (pm20) REVERT: W 26 PHE cc_start: 0.9437 (t80) cc_final: 0.9162 (t80) REVERT: W 35 LYS cc_start: 0.9747 (mtpp) cc_final: 0.9468 (mmmm) REVERT: W 52 MET cc_start: 0.9676 (mtp) cc_final: 0.9258 (ttm) REVERT: W 56 GLU cc_start: 0.9492 (tt0) cc_final: 0.9111 (tp30) REVERT: W 60 ASP cc_start: 0.9414 (m-30) cc_final: 0.9110 (m-30) REVERT: W 86 MET cc_start: 0.9667 (ptt) cc_final: 0.9420 (ptt) REVERT: W 120 PHE cc_start: 0.9504 (m-80) cc_final: 0.8970 (m-80) REVERT: X 16 THR cc_start: 0.8898 (m) cc_final: 0.8647 (m) REVERT: X 26 PHE cc_start: 0.9617 (t80) cc_final: 0.9083 (t80) REVERT: X 27 LEU cc_start: 0.9405 (mt) cc_final: 0.9025 (mt) REVERT: X 111 LYS cc_start: 0.9101 (mmpt) cc_final: 0.8897 (mmmt) REVERT: X 120 PHE cc_start: 0.9541 (m-80) cc_final: 0.9173 (m-10) REVERT: X 139 ASP cc_start: 0.9387 (m-30) cc_final: 0.9173 (m-30) outliers start: 10 outliers final: 1 residues processed: 1458 average time/residue: 0.4880 time to fit residues: 1061.1761 Evaluate side-chains 1123 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1122 time to evaluate : 3.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 303 optimal weight: 10.0000 chunk 323 optimal weight: 8.9990 chunk 194 optimal weight: 0.3980 chunk 140 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 292 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 322 optimal weight: 8.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 156 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS D 34 HIS D 129 HIS F 130 HIS F 156 GLN E 34 HIS E 130 HIS E 156 GLN G 129 HIS G 130 HIS H 34 HIS H 130 HIS I 76 HIS I 129 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 HIS K 129 HIS ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 HIS N 130 HIS ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 HIS ** R 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 HIS ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 HIS S 130 HIS S 156 GLN ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 156 GLN U 156 GLN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS V 130 HIS W 34 HIS W 129 HIS X 34 HIS X 129 HIS X 156 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.6967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32072 Z= 0.229 Angle : 0.765 21.537 43500 Z= 0.374 Chirality : 0.042 0.197 4829 Planarity : 0.004 0.050 5615 Dihedral : 7.997 87.357 4222 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.18 % Allowed : 1.23 % Favored : 98.58 % 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: -0.45 (0.13), residues: 3742 helix: 0.14 (0.09), residues: 2959 sheet: None (None), residues: 0 loop : -1.61 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 37 HIS 0.012 0.002 HIS S 130 PHE 0.053 0.003 PHE B 10 TYR 0.022 0.002 TYR N 133 ARG 0.008 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1497 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1491 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9718 (pt0) cc_final: 0.9478 (tp30) REVERT: A 23 ASN cc_start: 0.9790 (m-40) cc_final: 0.9521 (m-40) REVERT: A 26 PHE cc_start: 0.9642 (t80) cc_final: 0.9273 (t80) REVERT: A 71 TYR cc_start: 0.8832 (m-10) cc_final: 0.8106 (m-80) REVERT: A 111 LYS cc_start: 0.8969 (mmpt) cc_final: 0.8742 (mmmt) REVERT: A 120 PHE cc_start: 0.9104 (m-10) cc_final: 0.8846 (m-10) REVERT: B 2 GLN cc_start: 0.9552 (mt0) cc_final: 0.9329 (pm20) REVERT: B 23 ASN cc_start: 0.9556 (m-40) cc_final: 0.9245 (m-40) REVERT: B 26 PHE cc_start: 0.9378 (t80) cc_final: 0.8887 (t80) REVERT: B 27 LEU cc_start: 0.9043 (mt) cc_final: 0.8606 (mt) REVERT: B 34 HIS cc_start: 0.9242 (t-90) cc_final: 0.8999 (t-90) REVERT: B 35 LYS cc_start: 0.9771 (mtpp) cc_final: 0.9478 (mmmm) REVERT: B 56 GLU cc_start: 0.9489 (tt0) cc_final: 0.9262 (tp30) REVERT: B 86 MET cc_start: 0.9515 (pmm) cc_final: 0.9272 (pmm) REVERT: B 99 ASP cc_start: 0.9363 (p0) cc_final: 0.8919 (p0) REVERT: B 100 ARG cc_start: 0.9403 (mmt180) cc_final: 0.9134 (mmm160) REVERT: B 118 ASN cc_start: 0.9435 (t0) cc_final: 0.9148 (m110) REVERT: B 127 GLU cc_start: 0.9559 (mm-30) cc_final: 0.9290 (mm-30) REVERT: B 129 HIS cc_start: 0.9527 (m90) cc_final: 0.9283 (m90) REVERT: B 139 ASP cc_start: 0.9515 (m-30) cc_final: 0.9269 (m-30) REVERT: B 154 ILE cc_start: 0.9623 (pt) cc_final: 0.9392 (mm) REVERT: C 1 MET cc_start: 0.9452 (mmp) cc_final: 0.9242 (mmp) REVERT: C 26 PHE cc_start: 0.9681 (t80) cc_final: 0.9196 (t80) REVERT: C 27 LEU cc_start: 0.9504 (mt) cc_final: 0.9031 (mt) REVERT: C 33 ASP cc_start: 0.9015 (p0) cc_final: 0.8767 (p0) REVERT: C 108 MET cc_start: 0.9362 (ptt) cc_final: 0.8824 (ppp) REVERT: C 109 ARG cc_start: 0.9262 (ttt180) cc_final: 0.8901 (ttt180) REVERT: C 111 LYS cc_start: 0.9114 (mmpt) cc_final: 0.8866 (mmmt) REVERT: C 123 ILE cc_start: 0.9071 (tt) cc_final: 0.8778 (tt) REVERT: C 130 HIS cc_start: 0.9219 (t-90) cc_final: 0.8857 (t-170) REVERT: D 1 MET cc_start: 0.9040 (mmp) cc_final: 0.8270 (tmm) REVERT: D 2 GLN cc_start: 0.9633 (mt0) cc_final: 0.9431 (pm20) REVERT: D 27 LEU cc_start: 0.9348 (mt) cc_final: 0.9068 (mt) REVERT: D 101 LEU cc_start: 0.9574 (mt) cc_final: 0.9255 (mt) REVERT: D 109 ARG cc_start: 0.9310 (mtt180) cc_final: 0.9080 (tpm170) REVERT: D 120 PHE cc_start: 0.9554 (m-80) cc_final: 0.9057 (m-10) REVERT: F 23 ASN cc_start: 0.9677 (m-40) cc_final: 0.9282 (t0) REVERT: F 26 PHE cc_start: 0.9473 (t80) cc_final: 0.9229 (t80) REVERT: F 27 LEU cc_start: 0.9273 (mm) cc_final: 0.8342 (mm) REVERT: F 33 ASP cc_start: 0.9156 (p0) cc_final: 0.8943 (p0) REVERT: F 60 ASP cc_start: 0.9783 (p0) cc_final: 0.9557 (p0) REVERT: F 71 TYR cc_start: 0.9301 (m-10) cc_final: 0.8538 (m-80) REVERT: F 111 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8699 (mmmt) REVERT: F 120 PHE cc_start: 0.9303 (m-80) cc_final: 0.8887 (m-80) REVERT: F 139 ASP cc_start: 0.9301 (m-30) cc_final: 0.9085 (m-30) REVERT: E 26 PHE cc_start: 0.9559 (t80) cc_final: 0.9181 (t80) REVERT: E 27 LEU cc_start: 0.9169 (mt) cc_final: 0.8955 (mm) REVERT: E 35 LYS cc_start: 0.9764 (mmtt) cc_final: 0.9556 (mmmm) REVERT: E 98 ILE cc_start: 0.8893 (mm) cc_final: 0.8577 (mm) REVERT: E 120 PHE cc_start: 0.9476 (m-10) cc_final: 0.9225 (m-10) REVERT: E 129 HIS cc_start: 0.9491 (m90) cc_final: 0.9239 (m90) REVERT: E 130 HIS cc_start: 0.8967 (t-90) cc_final: 0.8561 (t-90) REVERT: E 139 ASP cc_start: 0.9544 (m-30) cc_final: 0.9302 (m-30) REVERT: G 2 GLN cc_start: 0.9546 (mt0) cc_final: 0.9344 (pm20) REVERT: G 23 ASN cc_start: 0.9674 (m-40) cc_final: 0.9434 (m-40) REVERT: G 26 PHE cc_start: 0.9533 (t80) cc_final: 0.9197 (t80) REVERT: G 71 TYR cc_start: 0.9388 (m-80) cc_final: 0.9049 (m-80) REVERT: G 86 MET cc_start: 0.9476 (pmm) cc_final: 0.9247 (pmm) REVERT: G 123 ILE cc_start: 0.9483 (mm) cc_final: 0.9114 (mm) REVERT: G 129 HIS cc_start: 0.9544 (m90) cc_final: 0.9251 (m90) REVERT: H 23 ASN cc_start: 0.9635 (m-40) cc_final: 0.9227 (t0) REVERT: H 26 PHE cc_start: 0.9593 (t80) cc_final: 0.9095 (t80) REVERT: H 27 LEU cc_start: 0.9179 (mt) cc_final: 0.8527 (mt) REVERT: H 52 MET cc_start: 0.8138 (mtt) cc_final: 0.7675 (mtt) REVERT: H 61 ARG cc_start: 0.9404 (tpt170) cc_final: 0.9151 (ttt180) REVERT: H 71 TYR cc_start: 0.9055 (m-80) cc_final: 0.8672 (m-80) REVERT: H 111 LYS cc_start: 0.9136 (mmmt) cc_final: 0.8843 (mmmt) REVERT: H 120 PHE cc_start: 0.9443 (m-10) cc_final: 0.9147 (m-10) REVERT: H 123 ILE cc_start: 0.9321 (tt) cc_final: 0.8635 (tt) REVERT: H 126 ASP cc_start: 0.9631 (m-30) cc_final: 0.9358 (m-30) REVERT: H 139 ASP cc_start: 0.9536 (m-30) cc_final: 0.9321 (m-30) REVERT: I 2 GLN cc_start: 0.9601 (mt0) cc_final: 0.9381 (mm-40) REVERT: I 6 GLU cc_start: 0.9598 (tp30) cc_final: 0.9257 (tp30) REVERT: I 9 GLU cc_start: 0.9690 (tp30) cc_final: 0.9463 (tp30) REVERT: I 23 ASN cc_start: 0.9513 (m-40) cc_final: 0.9266 (m-40) REVERT: I 24 GLN cc_start: 0.9473 (tt0) cc_final: 0.9175 (tm-30) REVERT: I 26 PHE cc_start: 0.9630 (t80) cc_final: 0.9152 (t80) REVERT: I 27 LEU cc_start: 0.9352 (mt) cc_final: 0.9008 (mt) REVERT: I 108 MET cc_start: 0.9722 (ptp) cc_final: 0.9410 (ptp) REVERT: I 120 PHE cc_start: 0.9543 (m-80) cc_final: 0.8861 (m-80) REVERT: J 26 PHE cc_start: 0.9623 (t80) cc_final: 0.9413 (t80) REVERT: J 27 LEU cc_start: 0.9308 (mt) cc_final: 0.9019 (mt) REVERT: J 52 MET cc_start: 0.8972 (mtm) cc_final: 0.8275 (mtt) REVERT: J 86 MET cc_start: 0.9539 (pmm) cc_final: 0.9328 (pmm) REVERT: J 111 LYS cc_start: 0.9145 (mmpt) cc_final: 0.8930 (mmmt) REVERT: K 26 PHE cc_start: 0.9489 (t80) cc_final: 0.9205 (t80) REVERT: K 73 ARG cc_start: 0.8223 (ptm-80) cc_final: 0.7763 (tmm160) REVERT: K 111 LYS cc_start: 0.8996 (mmpt) cc_final: 0.8731 (mmmt) REVERT: K 120 PHE cc_start: 0.9515 (m-80) cc_final: 0.8963 (m-80) REVERT: K 139 ASP cc_start: 0.9358 (m-30) cc_final: 0.9155 (m-30) REVERT: L 1 MET cc_start: 0.9415 (mmp) cc_final: 0.9149 (mmp) REVERT: L 23 ASN cc_start: 0.9564 (m-40) cc_final: 0.9161 (m-40) REVERT: L 26 PHE cc_start: 0.9586 (t80) cc_final: 0.9097 (t80) REVERT: L 27 LEU cc_start: 0.9510 (mt) cc_final: 0.8939 (mt) REVERT: L 34 HIS cc_start: 0.9331 (t70) cc_final: 0.9051 (t-90) REVERT: L 52 MET cc_start: 0.9563 (mtp) cc_final: 0.8659 (mtp) REVERT: L 53 ARG cc_start: 0.9178 (ttp-110) cc_final: 0.8926 (ptp-110) REVERT: L 61 ARG cc_start: 0.9715 (tpt170) cc_final: 0.9512 (ttt180) REVERT: L 108 MET cc_start: 0.8993 (ptt) cc_final: 0.8203 (ppp) REVERT: L 109 ARG cc_start: 0.9673 (mtp-110) cc_final: 0.9282 (ptp-110) REVERT: L 111 LYS cc_start: 0.9049 (mmpt) cc_final: 0.8847 (mmmt) REVERT: L 114 ILE cc_start: 0.9253 (mp) cc_final: 0.8940 (mp) REVERT: L 118 ASN cc_start: 0.9438 (t0) cc_final: 0.9182 (m-40) REVERT: L 130 HIS cc_start: 0.9153 (t-90) cc_final: 0.8811 (t-90) REVERT: M 1 MET cc_start: 0.9121 (mmm) cc_final: 0.8341 (tmm) REVERT: M 2 GLN cc_start: 0.9610 (mt0) cc_final: 0.9070 (pp30) REVERT: M 27 LEU cc_start: 0.9448 (mt) cc_final: 0.9208 (mt) REVERT: M 111 LYS cc_start: 0.9004 (mmpt) cc_final: 0.8788 (mmmt) REVERT: M 120 PHE cc_start: 0.9502 (m-80) cc_final: 0.9101 (m-10) REVERT: M 130 HIS cc_start: 0.9255 (t70) cc_final: 0.8950 (t70) REVERT: M 155 GLU cc_start: 0.9009 (tp30) cc_final: 0.8687 (mp0) REVERT: M 156 GLN cc_start: 0.6839 (tt0) cc_final: 0.5356 (tt0) REVERT: N 2 GLN cc_start: 0.9565 (mt0) cc_final: 0.9310 (pm20) REVERT: N 23 ASN cc_start: 0.9516 (m-40) cc_final: 0.9179 (t0) REVERT: N 26 PHE cc_start: 0.9431 (t80) cc_final: 0.9053 (t80) REVERT: N 27 LEU cc_start: 0.9334 (mt) cc_final: 0.8896 (mt) REVERT: N 34 HIS cc_start: 0.8195 (p90) cc_final: 0.7796 (p90) REVERT: N 61 ARG cc_start: 0.9784 (tpt-90) cc_final: 0.9511 (ttt180) REVERT: N 100 ARG cc_start: 0.9500 (mmm160) cc_final: 0.9295 (mmm-85) REVERT: N 120 PHE cc_start: 0.9636 (m-80) cc_final: 0.9412 (m-80) REVERT: O 26 PHE cc_start: 0.9559 (t80) cc_final: 0.9167 (t80) REVERT: O 27 LEU cc_start: 0.9371 (mp) cc_final: 0.8987 (mt) REVERT: O 32 GLN cc_start: 0.9395 (pt0) cc_final: 0.9156 (pt0) REVERT: O 102 ARG cc_start: 0.8413 (mtt180) cc_final: 0.7756 (mtp180) REVERT: O 108 MET cc_start: 0.9464 (mtt) cc_final: 0.8938 (ptp) REVERT: O 120 PHE cc_start: 0.9452 (m-80) cc_final: 0.9101 (m-80) REVERT: O 153 VAL cc_start: 0.9731 (m) cc_final: 0.9490 (p) REVERT: P 23 ASN cc_start: 0.9804 (m-40) cc_final: 0.9465 (m-40) REVERT: P 26 PHE cc_start: 0.9440 (t80) cc_final: 0.8893 (t80) REVERT: P 27 LEU cc_start: 0.9416 (mt) cc_final: 0.8875 (mt) REVERT: P 52 MET cc_start: 0.8740 (ttm) cc_final: 0.7951 (mmm) REVERT: P 73 ARG cc_start: 0.7360 (ptm-80) cc_final: 0.6926 (tmm160) REVERT: P 114 ILE cc_start: 0.8975 (mp) cc_final: 0.8601 (mp) REVERT: P 118 ASN cc_start: 0.9302 (t0) cc_final: 0.9054 (m110) REVERT: P 120 PHE cc_start: 0.9412 (m-80) cc_final: 0.8975 (m-80) REVERT: P 130 HIS cc_start: 0.9335 (t70) cc_final: 0.8974 (t70) REVERT: P 139 ASP cc_start: 0.9279 (m-30) cc_final: 0.9053 (m-30) REVERT: Q 1 MET cc_start: 0.9370 (mmp) cc_final: 0.9064 (mmp) REVERT: Q 23 ASN cc_start: 0.9633 (m-40) cc_final: 0.8962 (m-40) REVERT: Q 26 PHE cc_start: 0.9628 (t80) cc_final: 0.9188 (t80) REVERT: Q 27 LEU cc_start: 0.9464 (mt) cc_final: 0.9032 (mp) REVERT: Q 100 ARG cc_start: 0.9558 (mmm-85) cc_final: 0.9195 (mmm160) REVERT: Q 111 LYS cc_start: 0.8907 (mmpt) cc_final: 0.8692 (mmmt) REVERT: Q 130 HIS cc_start: 0.9124 (t-90) cc_final: 0.8745 (t-170) REVERT: Q 156 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6085 (tt0) REVERT: R 27 LEU cc_start: 0.9605 (tt) cc_final: 0.9286 (mt) REVERT: R 52 MET cc_start: 0.9065 (mtp) cc_final: 0.8538 (ttm) REVERT: R 114 ILE cc_start: 0.9047 (mm) cc_final: 0.8836 (mm) REVERT: R 118 ASN cc_start: 0.9471 (t0) cc_final: 0.9129 (m110) REVERT: R 139 ASP cc_start: 0.9513 (m-30) cc_final: 0.9282 (m-30) REVERT: R 155 GLU cc_start: 0.9057 (tp30) cc_final: 0.8461 (tm-30) REVERT: S 27 LEU cc_start: 0.9211 (mt) cc_final: 0.8964 (mt) REVERT: S 35 LYS cc_start: 0.9818 (tttt) cc_final: 0.9548 (tptp) REVERT: S 56 GLU cc_start: 0.9661 (tt0) cc_final: 0.9427 (tp30) REVERT: S 99 ASP cc_start: 0.9110 (p0) cc_final: 0.8657 (p0) REVERT: S 100 ARG cc_start: 0.9325 (mmm160) cc_final: 0.8937 (mmm160) REVERT: S 111 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8875 (mmmt) REVERT: S 120 PHE cc_start: 0.9334 (m-80) cc_final: 0.8817 (m-80) REVERT: T 108 MET cc_start: 0.9366 (tpt) cc_final: 0.8989 (tpt) REVERT: T 120 PHE cc_start: 0.9562 (m-10) cc_final: 0.9307 (m-10) REVERT: T 123 ILE cc_start: 0.9586 (pt) cc_final: 0.9307 (pt) REVERT: T 127 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9331 (mm-30) REVERT: T 130 HIS cc_start: 0.9494 (t70) cc_final: 0.9284 (t70) REVERT: T 139 ASP cc_start: 0.9412 (m-30) cc_final: 0.9159 (m-30) REVERT: U 24 GLN cc_start: 0.9627 (tt0) cc_final: 0.9334 (tp-100) REVERT: U 26 PHE cc_start: 0.9571 (t80) cc_final: 0.8860 (t80) REVERT: U 27 LEU cc_start: 0.9561 (tp) cc_final: 0.9018 (mt) REVERT: U 43 TYR cc_start: 0.8999 (m-80) cc_final: 0.8612 (m-80) REVERT: U 73 ARG cc_start: 0.8888 (ptm-80) cc_final: 0.8585 (ptm-80) REVERT: U 120 PHE cc_start: 0.9514 (m-80) cc_final: 0.9173 (m-80) REVERT: U 139 ASP cc_start: 0.9489 (m-30) cc_final: 0.9267 (m-30) REVERT: V 1 MET cc_start: 0.9476 (mmp) cc_final: 0.9117 (mmp) REVERT: V 23 ASN cc_start: 0.9649 (m-40) cc_final: 0.9342 (m-40) REVERT: V 26 PHE cc_start: 0.9657 (t80) cc_final: 0.9062 (t80) REVERT: V 27 LEU cc_start: 0.9417 (mt) cc_final: 0.8794 (mt) REVERT: V 102 ARG cc_start: 0.8265 (mtt180) cc_final: 0.7990 (mtp85) REVERT: V 111 LYS cc_start: 0.9063 (mmpt) cc_final: 0.8835 (mmmt) REVERT: V 120 PHE cc_start: 0.9584 (m-80) cc_final: 0.9016 (m-80) REVERT: V 139 ASP cc_start: 0.9345 (m-30) cc_final: 0.9099 (m-30) REVERT: W 1 MET cc_start: 0.9183 (mpp) cc_final: 0.8959 (mpp) REVERT: W 26 PHE cc_start: 0.9434 (t80) cc_final: 0.9123 (t80) REVERT: W 35 LYS cc_start: 0.9764 (mtpp) cc_final: 0.9490 (mmmm) REVERT: W 52 MET cc_start: 0.9665 (mtp) cc_final: 0.9177 (ttm) REVERT: W 56 GLU cc_start: 0.9479 (tt0) cc_final: 0.9103 (tp30) REVERT: W 60 ASP cc_start: 0.9399 (m-30) cc_final: 0.9128 (m-30) REVERT: W 86 MET cc_start: 0.9687 (ptt) cc_final: 0.9450 (ptt) REVERT: W 102 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7598 (mtt180) REVERT: W 111 LYS cc_start: 0.9230 (mmmt) cc_final: 0.8807 (mmmt) REVERT: W 120 PHE cc_start: 0.9492 (m-80) cc_final: 0.8988 (m-80) REVERT: W 127 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9142 (mm-30) REVERT: X 16 THR cc_start: 0.8766 (m) cc_final: 0.8506 (m) REVERT: X 26 PHE cc_start: 0.9642 (t80) cc_final: 0.9177 (t80) REVERT: X 27 LEU cc_start: 0.9376 (mt) cc_final: 0.9012 (mt) REVERT: X 120 PHE cc_start: 0.9547 (m-80) cc_final: 0.9166 (m-10) REVERT: X 139 ASP cc_start: 0.9360 (m-30) cc_final: 0.9146 (m-30) outliers start: 6 outliers final: 0 residues processed: 1491 average time/residue: 0.4853 time to fit residues: 1081.9909 Evaluate side-chains 1134 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1134 time to evaluate : 3.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 8.9990 chunk 341 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 358 optimal weight: 5.9990 chunk 330 optimal weight: 20.0000 chunk 285 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 220 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS B 156 GLN C 24 GLN C 28 HIS C 129 HIS C 156 GLN D 34 HIS F 129 HIS E 34 HIS E 156 GLN H 34 HIS I 129 HIS I 130 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 HIS K 28 HIS K 34 HIS K 129 HIS ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 HIS ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS O 129 HIS ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 HIS ** R 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS S 23 ASN S 34 HIS S 130 HIS ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 156 GLN U 156 GLN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS V 129 HIS W 34 HIS W 130 HIS X 34 HIS X 129 HIS X 156 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.7285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32072 Z= 0.201 Angle : 0.762 19.712 43500 Z= 0.370 Chirality : 0.042 0.303 4829 Planarity : 0.004 0.155 5615 Dihedral : 7.982 87.289 4222 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.18 % Allowed : 0.63 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 3742 helix: 0.16 (0.09), residues: 2928 sheet: None (None), residues: 0 loop : -1.55 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 37 HIS 0.012 0.001 HIS S 130 PHE 0.046 0.002 PHE U 10 TYR 0.021 0.001 TYR N 133 ARG 0.015 0.001 ARG R 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1546 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1540 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9704 (pt0) cc_final: 0.9478 (tp30) REVERT: A 23 ASN cc_start: 0.9776 (m-40) cc_final: 0.9355 (t0) REVERT: A 26 PHE cc_start: 0.9632 (t80) cc_final: 0.9296 (t80) REVERT: A 71 TYR cc_start: 0.8825 (m-10) cc_final: 0.8345 (m-80) REVERT: A 111 LYS cc_start: 0.8949 (mmpt) cc_final: 0.8735 (mmmt) REVERT: A 120 PHE cc_start: 0.9065 (m-10) cc_final: 0.8830 (m-10) REVERT: B 2 GLN cc_start: 0.9555 (mt0) cc_final: 0.9310 (pm20) REVERT: B 26 PHE cc_start: 0.9395 (t80) cc_final: 0.9025 (t80) REVERT: B 34 HIS cc_start: 0.9230 (t-90) cc_final: 0.9030 (t-90) REVERT: B 35 LYS cc_start: 0.9756 (mtpp) cc_final: 0.9454 (mmmm) REVERT: B 43 TYR cc_start: 0.9123 (m-80) cc_final: 0.8838 (m-80) REVERT: B 56 GLU cc_start: 0.9463 (tt0) cc_final: 0.9201 (tp30) REVERT: B 100 ARG cc_start: 0.9396 (mmt180) cc_final: 0.9152 (mmm160) REVERT: B 111 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8682 (mmmt) REVERT: B 126 ASP cc_start: 0.9516 (m-30) cc_final: 0.9307 (m-30) REVERT: B 127 GLU cc_start: 0.9606 (mm-30) cc_final: 0.9232 (mm-30) REVERT: B 137 GLN cc_start: 0.9801 (mm-40) cc_final: 0.9499 (tp-100) REVERT: B 139 ASP cc_start: 0.9506 (m-30) cc_final: 0.9265 (m-30) REVERT: B 154 ILE cc_start: 0.9681 (pt) cc_final: 0.9316 (mm) REVERT: C 1 MET cc_start: 0.9466 (mmp) cc_final: 0.9209 (mmp) REVERT: C 23 ASN cc_start: 0.9627 (m-40) cc_final: 0.9199 (t0) REVERT: C 26 PHE cc_start: 0.9665 (t80) cc_final: 0.9271 (t80) REVERT: C 27 LEU cc_start: 0.9455 (mt) cc_final: 0.9132 (mt) REVERT: C 33 ASP cc_start: 0.8997 (p0) cc_final: 0.8749 (p0) REVERT: C 111 LYS cc_start: 0.9069 (mmpt) cc_final: 0.8839 (mmmt) REVERT: C 130 HIS cc_start: 0.9231 (t-90) cc_final: 0.8904 (t-170) REVERT: C 139 ASP cc_start: 0.9195 (m-30) cc_final: 0.8952 (m-30) REVERT: D 1 MET cc_start: 0.8982 (mmp) cc_final: 0.8299 (tmm) REVERT: D 2 GLN cc_start: 0.9606 (mt0) cc_final: 0.9393 (pm20) REVERT: D 23 ASN cc_start: 0.9411 (m-40) cc_final: 0.8964 (m-40) REVERT: D 27 LEU cc_start: 0.9341 (mt) cc_final: 0.8946 (mt) REVERT: D 101 LEU cc_start: 0.9555 (mt) cc_final: 0.9266 (mt) REVERT: D 114 ILE cc_start: 0.8733 (mp) cc_final: 0.8527 (mp) REVERT: D 118 ASN cc_start: 0.9397 (t0) cc_final: 0.9082 (m110) REVERT: D 120 PHE cc_start: 0.9532 (m-80) cc_final: 0.9073 (m-10) REVERT: D 123 ILE cc_start: 0.9551 (tt) cc_final: 0.9340 (tt) REVERT: F 23 ASN cc_start: 0.9674 (m-40) cc_final: 0.9365 (t0) REVERT: F 27 LEU cc_start: 0.9250 (mm) cc_final: 0.8579 (mm) REVERT: F 33 ASP cc_start: 0.9112 (p0) cc_final: 0.8880 (p0) REVERT: F 60 ASP cc_start: 0.9766 (p0) cc_final: 0.9517 (p0) REVERT: F 71 TYR cc_start: 0.9302 (m-10) cc_final: 0.8378 (m-80) REVERT: F 102 ARG cc_start: 0.8396 (mtt180) cc_final: 0.7612 (mtp180) REVERT: F 111 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8658 (mmmt) REVERT: F 120 PHE cc_start: 0.9318 (m-80) cc_final: 0.8946 (m-80) REVERT: E 23 ASN cc_start: 0.9552 (m-40) cc_final: 0.9159 (t0) REVERT: E 26 PHE cc_start: 0.9538 (t80) cc_final: 0.9045 (t80) REVERT: E 27 LEU cc_start: 0.9183 (mt) cc_final: 0.8770 (mm) REVERT: E 35 LYS cc_start: 0.9756 (mmtt) cc_final: 0.9532 (mmmm) REVERT: E 98 ILE cc_start: 0.8811 (mm) cc_final: 0.8501 (mm) REVERT: E 130 HIS cc_start: 0.8891 (t-90) cc_final: 0.8445 (t-90) REVERT: E 139 ASP cc_start: 0.9526 (m-30) cc_final: 0.9319 (m-30) REVERT: E 141 ILE cc_start: 0.9718 (mt) cc_final: 0.9509 (mt) REVERT: G 2 GLN cc_start: 0.9562 (mt0) cc_final: 0.9341 (pm20) REVERT: G 23 ASN cc_start: 0.9669 (m-40) cc_final: 0.9447 (m-40) REVERT: G 26 PHE cc_start: 0.9527 (t80) cc_final: 0.9211 (t80) REVERT: G 71 TYR cc_start: 0.9368 (m-80) cc_final: 0.9076 (m-80) REVERT: G 72 GLN cc_start: 0.9684 (pm20) cc_final: 0.9464 (pm20) REVERT: G 86 MET cc_start: 0.9454 (pmm) cc_final: 0.9223 (pmm) REVERT: G 108 MET cc_start: 0.9489 (mtt) cc_final: 0.9259 (ptm) REVERT: G 123 ILE cc_start: 0.9432 (mm) cc_final: 0.9095 (mm) REVERT: G 129 HIS cc_start: 0.9429 (m90) cc_final: 0.9227 (m90) REVERT: H 23 ASN cc_start: 0.9632 (m-40) cc_final: 0.9298 (t0) REVERT: H 26 PHE cc_start: 0.9581 (t80) cc_final: 0.9180 (t80) REVERT: H 27 LEU cc_start: 0.9171 (mt) cc_final: 0.8726 (mt) REVERT: H 61 ARG cc_start: 0.9428 (tpt170) cc_final: 0.9206 (ttt180) REVERT: H 71 TYR cc_start: 0.8974 (m-80) cc_final: 0.8593 (m-80) REVERT: H 94 GLU cc_start: 0.9262 (mp0) cc_final: 0.8628 (mp0) REVERT: H 98 ILE cc_start: 0.9476 (tt) cc_final: 0.9201 (tt) REVERT: H 109 ARG cc_start: 0.9510 (mtp180) cc_final: 0.9282 (ptp-110) REVERT: H 111 LYS cc_start: 0.9121 (mmmt) cc_final: 0.8810 (mmmt) REVERT: H 120 PHE cc_start: 0.9418 (m-10) cc_final: 0.9182 (m-10) REVERT: H 139 ASP cc_start: 0.9533 (m-30) cc_final: 0.9324 (m-30) REVERT: I 6 GLU cc_start: 0.9585 (tp30) cc_final: 0.9249 (tp30) REVERT: I 9 GLU cc_start: 0.9654 (tp30) cc_final: 0.9437 (tp30) REVERT: I 23 ASN cc_start: 0.9473 (m-40) cc_final: 0.9074 (t0) REVERT: I 24 GLN cc_start: 0.9458 (tt0) cc_final: 0.9038 (tm-30) REVERT: I 26 PHE cc_start: 0.9621 (t80) cc_final: 0.9109 (t80) REVERT: I 27 LEU cc_start: 0.9305 (mt) cc_final: 0.8850 (mt) REVERT: I 78 ARG cc_start: 0.9406 (mtm-85) cc_final: 0.9091 (mpt180) REVERT: I 111 LYS cc_start: 0.8907 (mmpt) cc_final: 0.8679 (mmmt) REVERT: I 120 PHE cc_start: 0.9505 (m-80) cc_final: 0.9008 (m-80) REVERT: J 23 ASN cc_start: 0.9293 (m-40) cc_final: 0.8941 (t0) REVERT: J 52 MET cc_start: 0.8820 (mtm) cc_final: 0.8157 (mtt) REVERT: J 86 MET cc_start: 0.9472 (pmm) cc_final: 0.9259 (pmm) REVERT: J 102 ARG cc_start: 0.8317 (mtt180) cc_final: 0.7921 (ptm160) REVERT: K 26 PHE cc_start: 0.9450 (t80) cc_final: 0.9174 (t80) REVERT: K 73 ARG cc_start: 0.8307 (ptm-80) cc_final: 0.7802 (tmm160) REVERT: K 111 LYS cc_start: 0.8954 (mmpt) cc_final: 0.8679 (mmmt) REVERT: K 120 PHE cc_start: 0.9507 (m-80) cc_final: 0.8863 (m-80) REVERT: K 139 ASP cc_start: 0.9337 (m-30) cc_final: 0.9133 (m-30) REVERT: L 1 MET cc_start: 0.9330 (mmp) cc_final: 0.9075 (mmp) REVERT: L 23 ASN cc_start: 0.9526 (m-40) cc_final: 0.9049 (m-40) REVERT: L 26 PHE cc_start: 0.9558 (t80) cc_final: 0.9107 (t80) REVERT: L 27 LEU cc_start: 0.9532 (mt) cc_final: 0.9015 (mt) REVERT: L 34 HIS cc_start: 0.9286 (t70) cc_final: 0.8994 (t-90) REVERT: L 52 MET cc_start: 0.9528 (mtp) cc_final: 0.8659 (mtp) REVERT: L 53 ARG cc_start: 0.9150 (ttp-110) cc_final: 0.8896 (ptp-110) REVERT: L 109 ARG cc_start: 0.9675 (mtp-110) cc_final: 0.9422 (ptp-110) REVERT: L 130 HIS cc_start: 0.9234 (t-90) cc_final: 0.8896 (t-90) REVERT: M 1 MET cc_start: 0.9166 (mmm) cc_final: 0.8487 (tmm) REVERT: M 2 GLN cc_start: 0.9650 (mt0) cc_final: 0.9209 (pp30) REVERT: M 23 ASN cc_start: 0.9510 (m-40) cc_final: 0.9072 (t0) REVERT: M 27 LEU cc_start: 0.9400 (mt) cc_final: 0.9016 (mt) REVERT: M 52 MET cc_start: 0.8838 (mtm) cc_final: 0.8606 (ttm) REVERT: M 101 LEU cc_start: 0.9481 (mt) cc_final: 0.9281 (mt) REVERT: M 120 PHE cc_start: 0.9486 (m-80) cc_final: 0.9130 (m-10) REVERT: M 123 ILE cc_start: 0.9462 (tt) cc_final: 0.8793 (tt) REVERT: M 130 HIS cc_start: 0.9070 (t-90) cc_final: 0.8694 (t-90) REVERT: M 139 ASP cc_start: 0.9466 (m-30) cc_final: 0.9253 (m-30) REVERT: M 155 GLU cc_start: 0.8999 (tp30) cc_final: 0.8703 (mp0) REVERT: M 156 GLN cc_start: 0.6850 (tt0) cc_final: 0.5220 (tt0) REVERT: N 2 GLN cc_start: 0.9557 (mt0) cc_final: 0.9312 (pm20) REVERT: N 23 ASN cc_start: 0.9493 (m-40) cc_final: 0.9223 (t0) REVERT: N 26 PHE cc_start: 0.9450 (t80) cc_final: 0.9027 (t80) REVERT: N 34 HIS cc_start: 0.8124 (p90) cc_final: 0.7897 (p90) REVERT: N 35 LYS cc_start: 0.9726 (tptm) cc_final: 0.9423 (tptp) REVERT: N 61 ARG cc_start: 0.9756 (tpt-90) cc_final: 0.9474 (ttt180) REVERT: N 100 ARG cc_start: 0.9501 (mmm160) cc_final: 0.9282 (mmm-85) REVERT: N 108 MET cc_start: 0.9201 (ptt) cc_final: 0.8843 (ptt) REVERT: N 111 LYS cc_start: 0.8926 (mmpt) cc_final: 0.8719 (mmmt) REVERT: N 120 PHE cc_start: 0.9631 (m-80) cc_final: 0.9390 (m-80) REVERT: N 123 ILE cc_start: 0.9615 (mm) cc_final: 0.9413 (mm) REVERT: N 153 VAL cc_start: 0.9714 (m) cc_final: 0.9436 (p) REVERT: O 26 PHE cc_start: 0.9557 (t80) cc_final: 0.9205 (t80) REVERT: O 27 LEU cc_start: 0.9386 (mp) cc_final: 0.9027 (mp) REVERT: O 32 GLN cc_start: 0.9353 (pt0) cc_final: 0.9103 (pt0) REVERT: O 102 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7348 (mtp180) REVERT: O 108 MET cc_start: 0.9347 (mtt) cc_final: 0.8904 (ptp) REVERT: O 111 LYS cc_start: 0.9129 (mmpt) cc_final: 0.8884 (mmmt) REVERT: O 120 PHE cc_start: 0.9393 (m-80) cc_final: 0.9010 (m-80) REVERT: O 130 HIS cc_start: 0.9769 (t-170) cc_final: 0.9521 (t-170) REVERT: O 153 VAL cc_start: 0.9800 (m) cc_final: 0.9543 (p) REVERT: O 156 GLN cc_start: 0.7144 (pp30) cc_final: 0.6838 (pp30) REVERT: P 23 ASN cc_start: 0.9823 (m-40) cc_final: 0.9549 (m-40) REVERT: P 26 PHE cc_start: 0.9459 (t80) cc_final: 0.8893 (t80) REVERT: P 27 LEU cc_start: 0.9409 (mt) cc_final: 0.8956 (mt) REVERT: P 43 TYR cc_start: 0.9610 (t80) cc_final: 0.9298 (t80) REVERT: P 61 ARG cc_start: 0.9604 (tpt170) cc_final: 0.9393 (ttt180) REVERT: P 114 ILE cc_start: 0.8895 (mp) cc_final: 0.8448 (mp) REVERT: P 118 ASN cc_start: 0.9252 (t0) cc_final: 0.9012 (m110) REVERT: P 120 PHE cc_start: 0.9468 (m-80) cc_final: 0.9164 (m-80) REVERT: P 130 HIS cc_start: 0.9334 (t70) cc_final: 0.9005 (t70) REVERT: P 139 ASP cc_start: 0.9261 (m-30) cc_final: 0.9035 (m-30) REVERT: Q 1 MET cc_start: 0.9352 (mmp) cc_final: 0.8967 (mmp) REVERT: Q 23 ASN cc_start: 0.9579 (m-40) cc_final: 0.8848 (m-40) REVERT: Q 26 PHE cc_start: 0.9633 (t80) cc_final: 0.9186 (t80) REVERT: Q 27 LEU cc_start: 0.9506 (mt) cc_final: 0.9066 (mp) REVERT: Q 102 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7748 (mtp85) REVERT: Q 111 LYS cc_start: 0.8910 (mmpt) cc_final: 0.8686 (mmmt) REVERT: Q 130 HIS cc_start: 0.8986 (t-90) cc_final: 0.8700 (t-170) REVERT: R 27 LEU cc_start: 0.9567 (tt) cc_final: 0.9350 (mm) REVERT: R 52 MET cc_start: 0.9090 (mtp) cc_final: 0.8743 (ttm) REVERT: R 120 PHE cc_start: 0.9471 (m-80) cc_final: 0.9167 (m-80) REVERT: R 139 ASP cc_start: 0.9479 (m-30) cc_final: 0.9233 (m-30) REVERT: R 155 GLU cc_start: 0.9040 (tp30) cc_final: 0.8470 (tm-30) REVERT: S 23 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8764 (t0) REVERT: S 26 PHE cc_start: 0.9443 (t80) cc_final: 0.9184 (t80) REVERT: S 27 LEU cc_start: 0.9253 (mt) cc_final: 0.8855 (mt) REVERT: S 37 TRP cc_start: 0.7899 (m-10) cc_final: 0.7081 (m-10) REVERT: S 56 GLU cc_start: 0.9652 (tt0) cc_final: 0.9448 (tp30) REVERT: S 102 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7818 (mtp85) REVERT: S 111 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8741 (mmmt) REVERT: S 120 PHE cc_start: 0.9370 (m-80) cc_final: 0.8900 (m-80) REVERT: T 108 MET cc_start: 0.9319 (tpt) cc_final: 0.8987 (tpt) REVERT: T 120 PHE cc_start: 0.9593 (m-10) cc_final: 0.9315 (m-10) REVERT: T 123 ILE cc_start: 0.9619 (pt) cc_final: 0.9385 (mm) REVERT: T 130 HIS cc_start: 0.9515 (t70) cc_final: 0.9271 (t70) REVERT: T 139 ASP cc_start: 0.9395 (m-30) cc_final: 0.9132 (m-30) REVERT: U 24 GLN cc_start: 0.9687 (tt0) cc_final: 0.9369 (tp-100) REVERT: U 26 PHE cc_start: 0.9580 (t80) cc_final: 0.8866 (t80) REVERT: U 27 LEU cc_start: 0.9562 (tp) cc_final: 0.8989 (mt) REVERT: U 43 TYR cc_start: 0.8977 (m-80) cc_final: 0.8591 (m-80) REVERT: U 73 ARG cc_start: 0.8998 (ptm-80) cc_final: 0.8664 (ptm-80) REVERT: U 86 MET cc_start: 0.9523 (pmm) cc_final: 0.9239 (pmm) REVERT: U 100 ARG cc_start: 0.9504 (mmm160) cc_final: 0.9112 (mmm160) REVERT: U 120 PHE cc_start: 0.9508 (m-80) cc_final: 0.9082 (m-80) REVERT: U 123 ILE cc_start: 0.9383 (pt) cc_final: 0.9174 (pt) REVERT: U 139 ASP cc_start: 0.9451 (m-30) cc_final: 0.9205 (m-30) REVERT: V 1 MET cc_start: 0.9416 (mmp) cc_final: 0.9111 (mmp) REVERT: V 23 ASN cc_start: 0.9653 (m-40) cc_final: 0.9354 (m-40) REVERT: V 26 PHE cc_start: 0.9649 (t80) cc_final: 0.9064 (t80) REVERT: V 27 LEU cc_start: 0.9446 (mt) cc_final: 0.9188 (mt) REVERT: V 33 ASP cc_start: 0.8903 (p0) cc_final: 0.8699 (p0) REVERT: V 78 ARG cc_start: 0.9260 (mtm-85) cc_final: 0.8939 (mpt180) REVERT: V 102 ARG cc_start: 0.8108 (mtt180) cc_final: 0.7696 (ptp-170) REVERT: V 108 MET cc_start: 0.9334 (ptt) cc_final: 0.8634 (ppp) REVERT: V 111 LYS cc_start: 0.8987 (mmpt) cc_final: 0.8746 (mmmt) REVERT: V 120 PHE cc_start: 0.9561 (m-80) cc_final: 0.9107 (m-10) REVERT: V 139 ASP cc_start: 0.9320 (m-30) cc_final: 0.9090 (m-30) REVERT: W 26 PHE cc_start: 0.9389 (t80) cc_final: 0.9137 (t80) REVERT: W 32 GLN cc_start: 0.9138 (pt0) cc_final: 0.8834 (pt0) REVERT: W 33 ASP cc_start: 0.7605 (m-30) cc_final: 0.7380 (m-30) REVERT: W 35 LYS cc_start: 0.9750 (mtpp) cc_final: 0.9443 (mtpt) REVERT: W 52 MET cc_start: 0.9648 (mtp) cc_final: 0.8873 (ttm) REVERT: W 56 GLU cc_start: 0.9433 (tt0) cc_final: 0.9045 (tp30) REVERT: W 60 ASP cc_start: 0.9340 (m-30) cc_final: 0.9043 (m-30) REVERT: W 86 MET cc_start: 0.9607 (ptt) cc_final: 0.9301 (ptt) REVERT: W 102 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7873 (ptp-170) REVERT: W 111 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8670 (mmmt) REVERT: W 120 PHE cc_start: 0.9472 (m-80) cc_final: 0.8874 (m-80) REVERT: W 123 ILE cc_start: 0.9420 (pt) cc_final: 0.9075 (pt) REVERT: W 127 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9166 (mm-30) REVERT: X 16 THR cc_start: 0.8638 (m) cc_final: 0.8396 (m) REVERT: X 23 ASN cc_start: 0.9710 (m-40) cc_final: 0.9506 (m-40) REVERT: X 26 PHE cc_start: 0.9662 (t80) cc_final: 0.9202 (t80) REVERT: X 27 LEU cc_start: 0.9339 (mt) cc_final: 0.8881 (mt) REVERT: X 70 ASN cc_start: 0.9113 (t0) cc_final: 0.8825 (t0) REVERT: X 120 PHE cc_start: 0.9562 (m-80) cc_final: 0.9119 (m-80) REVERT: X 139 ASP cc_start: 0.9331 (m-30) cc_final: 0.9111 (m-30) outliers start: 6 outliers final: 1 residues processed: 1540 average time/residue: 0.4919 time to fit residues: 1126.9266 Evaluate side-chains 1202 residues out of total 3358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1200 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 8.9990 chunk 304 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 263 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 293 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS B 156 GLN C 129 HIS D 34 HIS D 129 HIS F 130 HIS E 34 HIS E 156 GLN G 130 HIS H 34 HIS H 130 HIS I 129 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 HIS K 34 HIS K 129 HIS ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 GLN ** O 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 129 HIS ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 HIS Q 118 ASN S 34 HIS S 130 HIS S 156 GLN ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 130 HIS U 118 ASN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 HIS W 34 HIS W 129 HIS X 34 HIS X 129 HIS X 130 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.072436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050969 restraints weight = 137372.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052753 restraints weight = 107711.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054204 restraints weight = 88957.756| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.7467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32072 Z= 0.202 Angle : 0.762 17.511 43500 Z= 0.370 Chirality : 0.042 0.333 4829 Planarity : 0.004 0.125 5615 Dihedral : 7.917 89.665 4222 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.12 % Allowed : 0.51 % Favored : 99.37 % 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: -0.39 (0.13), residues: 3742 helix: 0.16 (0.09), residues: 2908 sheet: None (None), residues: 0 loop : -1.36 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 37 HIS 0.015 0.001 HIS N 54 PHE 0.039 0.002 PHE P 10 TYR 0.018 0.001 TYR M 133 ARG 0.014 0.001 ARG R 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14343.99 seconds wall clock time: 255 minutes 22.95 seconds (15322.95 seconds total)