Starting phenix.real_space_refine (version: dev) on Mon Dec 19 03:00:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e8g_9005/12_2022/6e8g_9005.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e8g_9005/12_2022/6e8g_9005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e8g_9005/12_2022/6e8g_9005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e8g_9005/12_2022/6e8g_9005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e8g_9005/12_2022/6e8g_9005.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e8g_9005/12_2022/6e8g_9005.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "S ARG 61": "NH1" <-> "NH2" Residue "S ARG 82": "NH1" <-> "NH2" Residue "S ARG 109": "NH1" <-> "NH2" Residue "S ARG 164": "NH1" <-> "NH2" Residue "S TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 20": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 20": "NH1" <-> "NH2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K ARG 82": "NH1" <-> "NH2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K ARG 164": "NH1" <-> "NH2" Residue "K TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 20": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 82": "NH1" <-> "NH2" Residue "M ARG 109": "NH1" <-> "NH2" Residue "M ARG 164": "NH1" <-> "NH2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ARG 82": "NH1" <-> "NH2" Residue "O ARG 109": "NH1" <-> "NH2" Residue "O ARG 164": "NH1" <-> "NH2" Residue "O TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "Q ARG 61": "NH1" <-> "NH2" Residue "Q ARG 82": "NH1" <-> "NH2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "Q ARG 164": "NH1" <-> "NH2" Residue "Q TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 20": "NH1" <-> "NH2" Residue "V ARG 61": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V ARG 109": "NH1" <-> "NH2" Residue "V ARG 164": "NH1" <-> "NH2" Residue "V TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "X ARG 61": "NH1" <-> "NH2" Residue "X ARG 82": "NH1" <-> "NH2" Residue "X ARG 109": "NH1" <-> "NH2" Residue "X ARG 164": "NH1" <-> "NH2" Residue "X TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 20": "NH1" <-> "NH2" Residue "Z ARG 61": "NH1" <-> "NH2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z ARG 109": "NH1" <-> "NH2" Residue "Z ARG 164": "NH1" <-> "NH2" Residue "Z TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA ARG 20": "NH1" <-> "NH2" Residue "BA ARG 61": "NH1" <-> "NH2" Residue "BA ARG 82": "NH1" <-> "NH2" Residue "BA ARG 109": "NH1" <-> "NH2" Residue "BA ARG 164": "NH1" <-> "NH2" Residue "BA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA ARG 20": "NH1" <-> "NH2" Residue "DA ARG 61": "NH1" <-> "NH2" Residue "DA ARG 82": "NH1" <-> "NH2" Residue "DA ARG 109": "NH1" <-> "NH2" Residue "DA ARG 164": "NH1" <-> "NH2" Residue "DA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA ARG 20": "NH1" <-> "NH2" Residue "FA ARG 61": "NH1" <-> "NH2" Residue "FA ARG 82": "NH1" <-> "NH2" Residue "FA ARG 109": "NH1" <-> "NH2" Residue "FA ARG 164": "NH1" <-> "NH2" Residue "FA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA ARG 20": "NH1" <-> "NH2" Residue "HA ARG 61": "NH1" <-> "NH2" Residue "HA ARG 82": "NH1" <-> "NH2" Residue "HA ARG 109": "NH1" <-> "NH2" Residue "HA ARG 164": "NH1" <-> "NH2" Residue "HA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA ARG 20": "NH1" <-> "NH2" Residue "JA ARG 61": "NH1" <-> "NH2" Residue "JA ARG 82": "NH1" <-> "NH2" Residue "JA ARG 109": "NH1" <-> "NH2" Residue "JA ARG 164": "NH1" <-> "NH2" Residue "JA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA ARG 20": "NH1" <-> "NH2" Residue "LA ARG 61": "NH1" <-> "NH2" Residue "LA ARG 82": "NH1" <-> "NH2" Residue "LA ARG 109": "NH1" <-> "NH2" Residue "LA ARG 164": "NH1" <-> "NH2" Residue "LA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MA ARG 20": "NH1" <-> "NH2" Residue "NA ARG 61": "NH1" <-> "NH2" Residue "NA ARG 82": "NH1" <-> "NH2" Residue "NA ARG 109": "NH1" <-> "NH2" Residue "NA ARG 164": "NH1" <-> "NH2" Residue "NA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OA ARG 20": "NH1" <-> "NH2" Residue "PA ARG 61": "NH1" <-> "NH2" Residue "PA ARG 82": "NH1" <-> "NH2" Residue "PA ARG 109": "NH1" <-> "NH2" Residue "PA ARG 164": "NH1" <-> "NH2" Residue "PA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QA ARG 20": "NH1" <-> "NH2" Residue "RA ARG 61": "NH1" <-> "NH2" Residue "RA ARG 82": "NH1" <-> "NH2" Residue "RA ARG 109": "NH1" <-> "NH2" Residue "RA ARG 164": "NH1" <-> "NH2" Residue "RA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA ARG 20": "NH1" <-> "NH2" Residue "TA ARG 61": "NH1" <-> "NH2" Residue "TA ARG 82": "NH1" <-> "NH2" Residue "TA ARG 109": "NH1" <-> "NH2" Residue "TA ARG 164": "NH1" <-> "NH2" Residue "TA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UA ARG 20": "NH1" <-> "NH2" Residue "VA ARG 61": "NH1" <-> "NH2" Residue "VA ARG 82": "NH1" <-> "NH2" Residue "VA ARG 109": "NH1" <-> "NH2" Residue "VA ARG 164": "NH1" <-> "NH2" Residue "VA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WA ARG 20": "NH1" <-> "NH2" Residue "XA ARG 61": "NH1" <-> "NH2" Residue "XA ARG 82": "NH1" <-> "NH2" Residue "XA ARG 109": "NH1" <-> "NH2" Residue "XA ARG 164": "NH1" <-> "NH2" Residue "XA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA ARG 20": "NH1" <-> "NH2" Residue "ZA ARG 61": "NH1" <-> "NH2" Residue "ZA ARG 82": "NH1" <-> "NH2" Residue "ZA ARG 109": "NH1" <-> "NH2" Residue "ZA ARG 164": "NH1" <-> "NH2" Residue "ZA TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB ARG 20": "NH1" <-> "NH2" Residue "BB ARG 61": "NH1" <-> "NH2" Residue "BB ARG 82": "NH1" <-> "NH2" Residue "BB ARG 109": "NH1" <-> "NH2" Residue "BB ARG 164": "NH1" <-> "NH2" Residue "BB TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB ARG 20": "NH1" <-> "NH2" Residue "DB ARG 61": "NH1" <-> "NH2" Residue "DB ARG 82": "NH1" <-> "NH2" Residue "DB ARG 109": "NH1" <-> "NH2" Residue "DB ARG 164": "NH1" <-> "NH2" Residue "DB TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB ARG 20": "NH1" <-> "NH2" Residue "FB ARG 61": "NH1" <-> "NH2" Residue "FB ARG 82": "NH1" <-> "NH2" Residue "FB ARG 109": "NH1" <-> "NH2" Residue "FB ARG 164": "NH1" <-> "NH2" Residue "FB TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GB ARG 20": "NH1" <-> "NH2" Residue "HB ARG 61": "NH1" <-> "NH2" Residue "HB ARG 82": "NH1" <-> "NH2" Residue "HB ARG 109": "NH1" <-> "NH2" Residue "HB ARG 164": "NH1" <-> "NH2" Residue "HB TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IB ARG 20": "NH1" <-> "NH2" Residue "JB ARG 61": "NH1" <-> "NH2" Residue "JB ARG 82": "NH1" <-> "NH2" Residue "JB ARG 109": "NH1" <-> "NH2" Residue "JB ARG 164": "NH1" <-> "NH2" Residue "JB TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KB ARG 20": "NH1" <-> "NH2" Residue "LB ARG 61": "NH1" <-> "NH2" Residue "LB ARG 82": "NH1" <-> "NH2" Residue "LB ARG 109": "NH1" <-> "NH2" Residue "LB ARG 164": "NH1" <-> "NH2" Residue "LB TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MB ARG 20": "NH1" <-> "NH2" Residue "NB ARG 61": "NH1" <-> "NH2" Residue "NB ARG 82": "NH1" <-> "NH2" Residue "NB ARG 109": "NH1" <-> "NH2" Residue "NB ARG 164": "NH1" <-> "NH2" Residue "NB TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB ARG 20": "NH1" <-> "NH2" Residue "PB ARG 61": "NH1" <-> "NH2" Residue "PB ARG 82": "NH1" <-> "NH2" Residue "PB ARG 109": "NH1" <-> "NH2" Residue "PB ARG 164": "NH1" <-> "NH2" Residue "PB TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QB ARG 20": "NH1" <-> "NH2" Residue "RB ARG 61": "NH1" <-> "NH2" Residue "RB ARG 82": "NH1" <-> "NH2" Residue "RB ARG 109": "NH1" <-> "NH2" Residue "RB ARG 164": "NH1" <-> "NH2" Residue "RB TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB ARG 20": "NH1" <-> "NH2" Residue "TB ARG 61": "NH1" <-> "NH2" Residue "TB ARG 82": "NH1" <-> "NH2" Residue "TB ARG 109": "NH1" <-> "NH2" Residue "TB ARG 164": "NH1" <-> "NH2" Residue "TB TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UB ARG 20": "NH1" <-> "NH2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 97272 Number of models: 1 Model: "" Number of chains: 72 Chain: "S" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Y" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "AA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "BA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "CA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "DA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "EA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "FA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "GA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "HA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "IA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "JA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "KA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "LA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "MA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "NA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "OA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "PA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "QA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "RA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "SA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "TA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "UA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "VA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "WA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "XA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "YA" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "ZA" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "AB" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "BB" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "CB" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "DB" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "EB" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "FB" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "GB" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "HB" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "IB" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "JB" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "KB" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "LB" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "MB" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "NB" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "OB" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "PB" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "QB" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "RB" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "SB" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "TB" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "UB" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1353 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 42.49, per 1000 atoms: 0.44 Number of scatterers: 97272 At special positions: 0 Unit cell: (244.696, 245.534, 182.684, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 648 16.00 O 18432 8.00 N 17244 7.00 C 60948 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=0, symmetry=0 Time building additional restraints: 31.44 Conformation dependent library (CDL) restraints added in 11.2 seconds 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23904 Finding SS restraints... Secondary structure from input PDB file: 432 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'S' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYS S 38 " --> pdb=" O GLN S 34 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU S 39 " --> pdb=" O LYS S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 82 Processing helix chain 'S' and resid 82 through 89 Processing helix chain 'S' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLU S 98 " --> pdb=" O SER S 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER S 99 " --> pdb=" O GLY S 95 " (cutoff:3.500A) Proline residue: S 108 - end of helix Processing helix chain 'S' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILE S 119 " --> pdb=" O ALA S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 152 Processing helix chain 'S' and resid 158 through 174 Processing helix chain 'T' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYS T 30 " --> pdb=" O ASP T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 106 Processing helix chain 'T' and resid 107 through 140 removed outlier: 3.917A pdb=" N THR T 140 " --> pdb=" O MET T 136 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALA T 160 " --> pdb=" O MET T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 199 Processing helix chain 'A' and resid 7 through 47 removed outlier: 3.947A pdb=" N LYS A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 82 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLU A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILE A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 158 through 174 Processing helix chain 'B' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYS B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 106 Processing helix chain 'B' and resid 107 through 140 removed outlier: 3.917A pdb=" N THR B 140 " --> pdb=" O MET B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALA B 160 " --> pdb=" O MET B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 199 Processing helix chain 'C' and resid 7 through 47 removed outlier: 3.947A pdb=" N LYS C 38 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 82 Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 93 through 110 removed outlier: 4.531A pdb=" N GLU C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER C 99 " --> pdb=" O GLY C 95 " (cutoff:3.500A) Proline residue: C 108 - end of helix Processing helix chain 'C' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILE C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 152 Processing helix chain 'C' and resid 158 through 174 Processing helix chain 'D' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYS D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 106 Processing helix chain 'D' and resid 107 through 140 removed outlier: 3.916A pdb=" N THR D 140 " --> pdb=" O MET D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALA D 160 " --> pdb=" O MET D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 199 Processing helix chain 'E' and resid 7 through 47 removed outlier: 3.947A pdb=" N LYS E 38 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 82 Processing helix chain 'E' and resid 82 through 89 Processing helix chain 'E' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLU E 98 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) Proline residue: E 108 - end of helix Processing helix chain 'E' and resid 115 through 128 removed outlier: 4.324A pdb=" N ILE E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 152 Processing helix chain 'E' and resid 158 through 174 Processing helix chain 'F' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYS F 30 " --> pdb=" O ASP F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 106 Processing helix chain 'F' and resid 107 through 140 removed outlier: 3.917A pdb=" N THR F 140 " --> pdb=" O MET F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALA F 160 " --> pdb=" O MET F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 199 Processing helix chain 'G' and resid 7 through 47 removed outlier: 3.947A pdb=" N LYS G 38 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 82 Processing helix chain 'G' and resid 82 through 89 Processing helix chain 'G' and resid 93 through 110 removed outlier: 4.529A pdb=" N GLU G 98 " --> pdb=" O SER G 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER G 99 " --> pdb=" O GLY G 95 " (cutoff:3.500A) Proline residue: G 108 - end of helix Processing helix chain 'G' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILE G 119 " --> pdb=" O ALA G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 152 Processing helix chain 'G' and resid 158 through 174 Processing helix chain 'H' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYS H 30 " --> pdb=" O ASP H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 106 Processing helix chain 'H' and resid 107 through 140 removed outlier: 3.916A pdb=" N THR H 140 " --> pdb=" O MET H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALA H 160 " --> pdb=" O MET H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 199 Processing helix chain 'I' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYS I 38 " --> pdb=" O GLN I 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU I 39 " --> pdb=" O LYS I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 82 Processing helix chain 'I' and resid 82 through 89 Processing helix chain 'I' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLU I 98 " --> pdb=" O SER I 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER I 99 " --> pdb=" O GLY I 95 " (cutoff:3.500A) Proline residue: I 108 - end of helix Processing helix chain 'I' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILE I 119 " --> pdb=" O ALA I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 152 Processing helix chain 'I' and resid 158 through 174 Processing helix chain 'J' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYS J 30 " --> pdb=" O ASP J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 106 Processing helix chain 'J' and resid 107 through 140 removed outlier: 3.917A pdb=" N THR J 140 " --> pdb=" O MET J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALA J 160 " --> pdb=" O MET J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 199 Processing helix chain 'K' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYS K 38 " --> pdb=" O GLN K 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU K 39 " --> pdb=" O LYS K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 82 Processing helix chain 'K' and resid 82 through 89 Processing helix chain 'K' and resid 93 through 110 removed outlier: 4.531A pdb=" N GLU K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SER K 99 " --> pdb=" O GLY K 95 " (cutoff:3.500A) Proline residue: K 108 - end of helix Processing helix chain 'K' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILE K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 152 Processing helix chain 'K' and resid 158 through 174 Processing helix chain 'L' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYS L 30 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 106 Processing helix chain 'L' and resid 107 through 140 removed outlier: 3.917A pdb=" N THR L 140 " --> pdb=" O MET L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALA L 160 " --> pdb=" O MET L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 199 Processing helix chain 'M' and resid 7 through 47 removed outlier: 3.947A pdb=" N LYS M 38 " --> pdb=" O GLN M 34 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU M 39 " --> pdb=" O LYS M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 82 Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLU M 98 " --> pdb=" O SER M 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER M 99 " --> pdb=" O GLY M 95 " (cutoff:3.500A) Proline residue: M 108 - end of helix Processing helix chain 'M' and resid 115 through 128 removed outlier: 4.324A pdb=" N ILE M 119 " --> pdb=" O ALA M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 152 Processing helix chain 'M' and resid 158 through 174 Processing helix chain 'N' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYS N 30 " --> pdb=" O ASP N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 106 Processing helix chain 'N' and resid 107 through 140 removed outlier: 3.917A pdb=" N THR N 140 " --> pdb=" O MET N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALA N 160 " --> pdb=" O MET N 156 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 199 Processing helix chain 'O' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYS O 38 " --> pdb=" O GLN O 34 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU O 39 " --> pdb=" O LYS O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 82 Processing helix chain 'O' and resid 82 through 89 Processing helix chain 'O' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLU O 98 " --> pdb=" O SER O 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER O 99 " --> pdb=" O GLY O 95 " (cutoff:3.500A) Proline residue: O 108 - end of helix Processing helix chain 'O' and resid 115 through 128 removed outlier: 4.322A pdb=" N ILE O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 152 Processing helix chain 'O' and resid 158 through 174 Processing helix chain 'P' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYS P 30 " --> pdb=" O ASP P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 106 Processing helix chain 'P' and resid 107 through 140 removed outlier: 3.916A pdb=" N THR P 140 " --> pdb=" O MET P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALA P 160 " --> pdb=" O MET P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 199 Processing helix chain 'Q' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYS Q 38 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU Q 39 " --> pdb=" O LYS Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 82 Processing helix chain 'Q' and resid 82 through 89 Processing helix chain 'Q' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLU Q 98 " --> pdb=" O SER Q 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER Q 99 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) Proline residue: Q 108 - end of helix Processing helix chain 'Q' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILE Q 119 " --> pdb=" O ALA Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 152 Processing helix chain 'Q' and resid 158 through 174 Processing helix chain 'R' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYS R 30 " --> pdb=" O ASP R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 106 Processing helix chain 'R' and resid 107 through 140 removed outlier: 3.917A pdb=" N THR R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALA R 160 " --> pdb=" O MET R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 199 Processing helix chain 'V' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYS V 38 " --> pdb=" O GLN V 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU V 39 " --> pdb=" O LYS V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 82 Processing helix chain 'V' and resid 82 through 89 Processing helix chain 'V' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLU V 98 " --> pdb=" O SER V 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER V 99 " --> pdb=" O GLY V 95 " (cutoff:3.500A) Proline residue: V 108 - end of helix Processing helix chain 'V' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILE V 119 " --> pdb=" O ALA V 115 " (cutoff:3.500A) Processing helix chain 'V' and resid 145 through 152 Processing helix chain 'V' and resid 158 through 174 Processing helix chain 'W' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYS W 30 " --> pdb=" O ASP W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 106 Processing helix chain 'W' and resid 107 through 140 removed outlier: 3.917A pdb=" N THR W 140 " --> pdb=" O MET W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALA W 160 " --> pdb=" O MET W 156 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 199 Processing helix chain 'X' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYS X 38 " --> pdb=" O GLN X 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU X 39 " --> pdb=" O LYS X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 82 Processing helix chain 'X' and resid 82 through 89 Processing helix chain 'X' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLU X 98 " --> pdb=" O SER X 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER X 99 " --> pdb=" O GLY X 95 " (cutoff:3.500A) Proline residue: X 108 - end of helix Processing helix chain 'X' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILE X 119 " --> pdb=" O ALA X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 152 Processing helix chain 'X' and resid 158 through 174 Processing helix chain 'Y' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYS Y 30 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 106 Processing helix chain 'Y' and resid 107 through 140 removed outlier: 3.917A pdb=" N THR Y 140 " --> pdb=" O MET Y 136 " (cutoff:3.500A) Processing helix chain 'Y' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALA Y 160 " --> pdb=" O MET Y 156 " (cutoff:3.500A) Processing helix chain 'Y' and resid 188 through 199 Processing helix chain 'Z' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYS Z 38 " --> pdb=" O GLN Z 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 82 Processing helix chain 'Z' and resid 82 through 89 Processing helix chain 'Z' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLU Z 98 " --> pdb=" O SER Z 94 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER Z 99 " --> pdb=" O GLY Z 95 " (cutoff:3.500A) Proline residue: Z 108 - end of helix Processing helix chain 'Z' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILE Z 119 " --> pdb=" O ALA Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 145 through 152 Processing helix chain 'Z' and resid 158 through 174 Processing helix chain 'AA' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYSAA 30 " --> pdb=" O ASPAA 26 " (cutoff:3.500A) Processing helix chain 'AA' and resid 44 through 106 Processing helix chain 'AA' and resid 107 through 140 removed outlier: 3.916A pdb=" N THRAA 140 " --> pdb=" O METAA 136 " (cutoff:3.500A) Processing helix chain 'AA' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALAAA 160 " --> pdb=" O METAA 156 " (cutoff:3.500A) Processing helix chain 'AA' and resid 188 through 199 Processing helix chain 'BA' and resid 7 through 47 removed outlier: 3.947A pdb=" N LYSBA 38 " --> pdb=" O GLNBA 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUBA 39 " --> pdb=" O LYSBA 35 " (cutoff:3.500A) Processing helix chain 'BA' and resid 49 through 82 Processing helix chain 'BA' and resid 82 through 89 Processing helix chain 'BA' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUBA 98 " --> pdb=" O SERBA 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERBA 99 " --> pdb=" O GLYBA 95 " (cutoff:3.500A) Proline residue: BA 108 - end of helix Processing helix chain 'BA' and resid 115 through 128 removed outlier: 4.324A pdb=" N ILEBA 119 " --> pdb=" O ALABA 115 " (cutoff:3.500A) Processing helix chain 'BA' and resid 145 through 152 Processing helix chain 'BA' and resid 158 through 174 Processing helix chain 'CA' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYSCA 30 " --> pdb=" O ASPCA 26 " (cutoff:3.500A) Processing helix chain 'CA' and resid 44 through 106 Processing helix chain 'CA' and resid 107 through 140 removed outlier: 3.916A pdb=" N THRCA 140 " --> pdb=" O METCA 136 " (cutoff:3.500A) Processing helix chain 'CA' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALACA 160 " --> pdb=" O METCA 156 " (cutoff:3.500A) Processing helix chain 'CA' and resid 188 through 199 Processing helix chain 'DA' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSDA 38 " --> pdb=" O GLNDA 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUDA 39 " --> pdb=" O LYSDA 35 " (cutoff:3.500A) Processing helix chain 'DA' and resid 49 through 82 Processing helix chain 'DA' and resid 82 through 89 Processing helix chain 'DA' and resid 93 through 110 removed outlier: 4.531A pdb=" N GLUDA 98 " --> pdb=" O SERDA 94 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SERDA 99 " --> pdb=" O GLYDA 95 " (cutoff:3.500A) Proline residue: DA 108 - end of helix Processing helix chain 'DA' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILEDA 119 " --> pdb=" O ALADA 115 " (cutoff:3.500A) Processing helix chain 'DA' and resid 145 through 152 Processing helix chain 'DA' and resid 158 through 174 Processing helix chain 'EA' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYSEA 30 " --> pdb=" O ASPEA 26 " (cutoff:3.500A) Processing helix chain 'EA' and resid 44 through 106 Processing helix chain 'EA' and resid 107 through 140 removed outlier: 3.916A pdb=" N THREA 140 " --> pdb=" O METEA 136 " (cutoff:3.500A) Processing helix chain 'EA' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALAEA 160 " --> pdb=" O METEA 156 " (cutoff:3.500A) Processing helix chain 'EA' and resid 188 through 199 Processing helix chain 'FA' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSFA 38 " --> pdb=" O GLNFA 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUFA 39 " --> pdb=" O LYSFA 35 " (cutoff:3.500A) Processing helix chain 'FA' and resid 49 through 82 Processing helix chain 'FA' and resid 82 through 89 Processing helix chain 'FA' and resid 93 through 110 removed outlier: 4.531A pdb=" N GLUFA 98 " --> pdb=" O SERFA 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERFA 99 " --> pdb=" O GLYFA 95 " (cutoff:3.500A) Proline residue: FA 108 - end of helix Processing helix chain 'FA' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILEFA 119 " --> pdb=" O ALAFA 115 " (cutoff:3.500A) Processing helix chain 'FA' and resid 145 through 152 Processing helix chain 'FA' and resid 158 through 174 Processing helix chain 'GA' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYSGA 30 " --> pdb=" O ASPGA 26 " (cutoff:3.500A) Processing helix chain 'GA' and resid 44 through 106 Processing helix chain 'GA' and resid 107 through 140 removed outlier: 3.917A pdb=" N THRGA 140 " --> pdb=" O METGA 136 " (cutoff:3.500A) Processing helix chain 'GA' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALAGA 160 " --> pdb=" O METGA 156 " (cutoff:3.500A) Processing helix chain 'GA' and resid 188 through 199 Processing helix chain 'HA' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSHA 38 " --> pdb=" O GLNHA 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUHA 39 " --> pdb=" O LYSHA 35 " (cutoff:3.500A) Processing helix chain 'HA' and resid 49 through 82 Processing helix chain 'HA' and resid 82 through 89 Processing helix chain 'HA' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUHA 98 " --> pdb=" O SERHA 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERHA 99 " --> pdb=" O GLYHA 95 " (cutoff:3.500A) Proline residue: HA 108 - end of helix Processing helix chain 'HA' and resid 115 through 128 removed outlier: 4.324A pdb=" N ILEHA 119 " --> pdb=" O ALAHA 115 " (cutoff:3.500A) Processing helix chain 'HA' and resid 145 through 152 Processing helix chain 'HA' and resid 158 through 174 Processing helix chain 'IA' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYSIA 30 " --> pdb=" O ASPIA 26 " (cutoff:3.500A) Processing helix chain 'IA' and resid 44 through 106 Processing helix chain 'IA' and resid 107 through 140 removed outlier: 3.917A pdb=" N THRIA 140 " --> pdb=" O METIA 136 " (cutoff:3.500A) Processing helix chain 'IA' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALAIA 160 " --> pdb=" O METIA 156 " (cutoff:3.500A) Processing helix chain 'IA' and resid 188 through 199 Processing helix chain 'JA' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSJA 38 " --> pdb=" O GLNJA 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUJA 39 " --> pdb=" O LYSJA 35 " (cutoff:3.500A) Processing helix chain 'JA' and resid 49 through 82 Processing helix chain 'JA' and resid 82 through 89 Processing helix chain 'JA' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUJA 98 " --> pdb=" O SERJA 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERJA 99 " --> pdb=" O GLYJA 95 " (cutoff:3.500A) Proline residue: JA 108 - end of helix Processing helix chain 'JA' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILEJA 119 " --> pdb=" O ALAJA 115 " (cutoff:3.500A) Processing helix chain 'JA' and resid 145 through 152 Processing helix chain 'JA' and resid 158 through 174 Processing helix chain 'KA' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYSKA 30 " --> pdb=" O ASPKA 26 " (cutoff:3.500A) Processing helix chain 'KA' and resid 44 through 106 Processing helix chain 'KA' and resid 107 through 140 removed outlier: 3.916A pdb=" N THRKA 140 " --> pdb=" O METKA 136 " (cutoff:3.500A) Processing helix chain 'KA' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALAKA 160 " --> pdb=" O METKA 156 " (cutoff:3.500A) Processing helix chain 'KA' and resid 188 through 199 Processing helix chain 'LA' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSLA 38 " --> pdb=" O GLNLA 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLULA 39 " --> pdb=" O LYSLA 35 " (cutoff:3.500A) Processing helix chain 'LA' and resid 49 through 82 Processing helix chain 'LA' and resid 82 through 89 Processing helix chain 'LA' and resid 93 through 110 removed outlier: 4.529A pdb=" N GLULA 98 " --> pdb=" O SERLA 94 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SERLA 99 " --> pdb=" O GLYLA 95 " (cutoff:3.500A) Proline residue: LA 108 - end of helix Processing helix chain 'LA' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILELA 119 " --> pdb=" O ALALA 115 " (cutoff:3.500A) Processing helix chain 'LA' and resid 145 through 152 Processing helix chain 'LA' and resid 158 through 174 Processing helix chain 'MA' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYSMA 30 " --> pdb=" O ASPMA 26 " (cutoff:3.500A) Processing helix chain 'MA' and resid 44 through 106 Processing helix chain 'MA' and resid 107 through 140 removed outlier: 3.916A pdb=" N THRMA 140 " --> pdb=" O METMA 136 " (cutoff:3.500A) Processing helix chain 'MA' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALAMA 160 " --> pdb=" O METMA 156 " (cutoff:3.500A) Processing helix chain 'MA' and resid 188 through 199 Processing helix chain 'NA' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSNA 38 " --> pdb=" O GLNNA 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUNA 39 " --> pdb=" O LYSNA 35 " (cutoff:3.500A) Processing helix chain 'NA' and resid 49 through 82 Processing helix chain 'NA' and resid 82 through 89 Processing helix chain 'NA' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUNA 98 " --> pdb=" O SERNA 94 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SERNA 99 " --> pdb=" O GLYNA 95 " (cutoff:3.500A) Proline residue: NA 108 - end of helix Processing helix chain 'NA' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILENA 119 " --> pdb=" O ALANA 115 " (cutoff:3.500A) Processing helix chain 'NA' and resid 145 through 152 Processing helix chain 'NA' and resid 158 through 174 Processing helix chain 'OA' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYSOA 30 " --> pdb=" O ASPOA 26 " (cutoff:3.500A) Processing helix chain 'OA' and resid 44 through 106 Processing helix chain 'OA' and resid 107 through 140 removed outlier: 3.916A pdb=" N THROA 140 " --> pdb=" O METOA 136 " (cutoff:3.500A) Processing helix chain 'OA' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALAOA 160 " --> pdb=" O METOA 156 " (cutoff:3.500A) Processing helix chain 'OA' and resid 188 through 199 Processing helix chain 'PA' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSPA 38 " --> pdb=" O GLNPA 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUPA 39 " --> pdb=" O LYSPA 35 " (cutoff:3.500A) Processing helix chain 'PA' and resid 49 through 82 Processing helix chain 'PA' and resid 82 through 89 Processing helix chain 'PA' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUPA 98 " --> pdb=" O SERPA 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERPA 99 " --> pdb=" O GLYPA 95 " (cutoff:3.500A) Proline residue: PA 108 - end of helix Processing helix chain 'PA' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILEPA 119 " --> pdb=" O ALAPA 115 " (cutoff:3.500A) Processing helix chain 'PA' and resid 145 through 152 Processing helix chain 'PA' and resid 158 through 174 Processing helix chain 'QA' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYSQA 30 " --> pdb=" O ASPQA 26 " (cutoff:3.500A) Processing helix chain 'QA' and resid 44 through 106 Processing helix chain 'QA' and resid 107 through 140 removed outlier: 3.916A pdb=" N THRQA 140 " --> pdb=" O METQA 136 " (cutoff:3.500A) Processing helix chain 'QA' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALAQA 160 " --> pdb=" O METQA 156 " (cutoff:3.500A) Processing helix chain 'QA' and resid 188 through 199 Processing helix chain 'RA' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSRA 38 " --> pdb=" O GLNRA 34 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLURA 39 " --> pdb=" O LYSRA 35 " (cutoff:3.500A) Processing helix chain 'RA' and resid 49 through 82 Processing helix chain 'RA' and resid 82 through 89 Processing helix chain 'RA' and resid 93 through 110 removed outlier: 4.529A pdb=" N GLURA 98 " --> pdb=" O SERRA 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERRA 99 " --> pdb=" O GLYRA 95 " (cutoff:3.500A) Proline residue: RA 108 - end of helix Processing helix chain 'RA' and resid 115 through 128 removed outlier: 4.322A pdb=" N ILERA 119 " --> pdb=" O ALARA 115 " (cutoff:3.500A) Processing helix chain 'RA' and resid 145 through 152 Processing helix chain 'RA' and resid 158 through 174 Processing helix chain 'SA' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYSSA 30 " --> pdb=" O ASPSA 26 " (cutoff:3.500A) Processing helix chain 'SA' and resid 44 through 106 Processing helix chain 'SA' and resid 107 through 140 removed outlier: 3.916A pdb=" N THRSA 140 " --> pdb=" O METSA 136 " (cutoff:3.500A) Processing helix chain 'SA' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALASA 160 " --> pdb=" O METSA 156 " (cutoff:3.500A) Processing helix chain 'SA' and resid 188 through 199 Processing helix chain 'TA' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSTA 38 " --> pdb=" O GLNTA 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUTA 39 " --> pdb=" O LYSTA 35 " (cutoff:3.500A) Processing helix chain 'TA' and resid 49 through 82 Processing helix chain 'TA' and resid 82 through 89 Processing helix chain 'TA' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUTA 98 " --> pdb=" O SERTA 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERTA 99 " --> pdb=" O GLYTA 95 " (cutoff:3.500A) Proline residue: TA 108 - end of helix Processing helix chain 'TA' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILETA 119 " --> pdb=" O ALATA 115 " (cutoff:3.500A) Processing helix chain 'TA' and resid 145 through 152 Processing helix chain 'TA' and resid 158 through 174 Processing helix chain 'UA' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYSUA 30 " --> pdb=" O ASPUA 26 " (cutoff:3.500A) Processing helix chain 'UA' and resid 44 through 106 Processing helix chain 'UA' and resid 107 through 140 removed outlier: 3.916A pdb=" N THRUA 140 " --> pdb=" O METUA 136 " (cutoff:3.500A) Processing helix chain 'UA' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALAUA 160 " --> pdb=" O METUA 156 " (cutoff:3.500A) Processing helix chain 'UA' and resid 188 through 199 Processing helix chain 'VA' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSVA 38 " --> pdb=" O GLNVA 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUVA 39 " --> pdb=" O LYSVA 35 " (cutoff:3.500A) Processing helix chain 'VA' and resid 49 through 82 Processing helix chain 'VA' and resid 82 through 89 Processing helix chain 'VA' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUVA 98 " --> pdb=" O SERVA 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERVA 99 " --> pdb=" O GLYVA 95 " (cutoff:3.500A) Proline residue: VA 108 - end of helix Processing helix chain 'VA' and resid 115 through 128 removed outlier: 4.322A pdb=" N ILEVA 119 " --> pdb=" O ALAVA 115 " (cutoff:3.500A) Processing helix chain 'VA' and resid 145 through 152 Processing helix chain 'VA' and resid 158 through 174 Processing helix chain 'WA' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYSWA 30 " --> pdb=" O ASPWA 26 " (cutoff:3.500A) Processing helix chain 'WA' and resid 44 through 106 Processing helix chain 'WA' and resid 107 through 140 removed outlier: 3.916A pdb=" N THRWA 140 " --> pdb=" O METWA 136 " (cutoff:3.500A) Processing helix chain 'WA' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALAWA 160 " --> pdb=" O METWA 156 " (cutoff:3.500A) Processing helix chain 'WA' and resid 188 through 199 Processing helix chain 'XA' and resid 7 through 47 removed outlier: 3.947A pdb=" N LYSXA 38 " --> pdb=" O GLNXA 34 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLUXA 39 " --> pdb=" O LYSXA 35 " (cutoff:3.500A) Processing helix chain 'XA' and resid 49 through 82 Processing helix chain 'XA' and resid 82 through 89 Processing helix chain 'XA' and resid 93 through 110 removed outlier: 4.529A pdb=" N GLUXA 98 " --> pdb=" O SERXA 94 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SERXA 99 " --> pdb=" O GLYXA 95 " (cutoff:3.500A) Proline residue: XA 108 - end of helix Processing helix chain 'XA' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILEXA 119 " --> pdb=" O ALAXA 115 " (cutoff:3.500A) Processing helix chain 'XA' and resid 145 through 152 Processing helix chain 'XA' and resid 158 through 174 Processing helix chain 'YA' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYSYA 30 " --> pdb=" O ASPYA 26 " (cutoff:3.500A) Processing helix chain 'YA' and resid 44 through 106 Processing helix chain 'YA' and resid 107 through 140 removed outlier: 3.917A pdb=" N THRYA 140 " --> pdb=" O METYA 136 " (cutoff:3.500A) Processing helix chain 'YA' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALAYA 160 " --> pdb=" O METYA 156 " (cutoff:3.500A) Processing helix chain 'YA' and resid 188 through 199 Processing helix chain 'ZA' and resid 7 through 47 removed outlier: 3.947A pdb=" N LYSZA 38 " --> pdb=" O GLNZA 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUZA 39 " --> pdb=" O LYSZA 35 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 49 through 82 Processing helix chain 'ZA' and resid 82 through 89 Processing helix chain 'ZA' and resid 93 through 110 removed outlier: 4.529A pdb=" N GLUZA 98 " --> pdb=" O SERZA 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERZA 99 " --> pdb=" O GLYZA 95 " (cutoff:3.500A) Proline residue: ZA 108 - end of helix Processing helix chain 'ZA' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILEZA 119 " --> pdb=" O ALAZA 115 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 145 through 152 Processing helix chain 'ZA' and resid 158 through 174 Processing helix chain 'AB' and resid 5 through 43 removed outlier: 3.623A pdb=" N LYSAB 30 " --> pdb=" O ASPAB 26 " (cutoff:3.500A) Processing helix chain 'AB' and resid 44 through 106 Processing helix chain 'AB' and resid 107 through 140 removed outlier: 3.917A pdb=" N THRAB 140 " --> pdb=" O METAB 136 " (cutoff:3.500A) Processing helix chain 'AB' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALAAB 160 " --> pdb=" O METAB 156 " (cutoff:3.500A) Processing helix chain 'AB' and resid 188 through 199 Processing helix chain 'BB' and resid 7 through 47 removed outlier: 3.947A pdb=" N LYSBB 38 " --> pdb=" O GLNBB 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUBB 39 " --> pdb=" O LYSBB 35 " (cutoff:3.500A) Processing helix chain 'BB' and resid 49 through 82 Processing helix chain 'BB' and resid 82 through 89 Processing helix chain 'BB' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUBB 98 " --> pdb=" O SERBB 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERBB 99 " --> pdb=" O GLYBB 95 " (cutoff:3.500A) Proline residue: BB 108 - end of helix Processing helix chain 'BB' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILEBB 119 " --> pdb=" O ALABB 115 " (cutoff:3.500A) Processing helix chain 'BB' and resid 145 through 152 Processing helix chain 'BB' and resid 158 through 174 Processing helix chain 'CB' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYSCB 30 " --> pdb=" O ASPCB 26 " (cutoff:3.500A) Processing helix chain 'CB' and resid 44 through 106 Processing helix chain 'CB' and resid 107 through 140 removed outlier: 3.916A pdb=" N THRCB 140 " --> pdb=" O METCB 136 " (cutoff:3.500A) Processing helix chain 'CB' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALACB 160 " --> pdb=" O METCB 156 " (cutoff:3.500A) Processing helix chain 'CB' and resid 188 through 199 Processing helix chain 'DB' and resid 7 through 47 removed outlier: 3.949A pdb=" N LYSDB 38 " --> pdb=" O GLNDB 34 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLUDB 39 " --> pdb=" O LYSDB 35 " (cutoff:3.500A) Processing helix chain 'DB' and resid 49 through 82 Processing helix chain 'DB' and resid 82 through 89 Processing helix chain 'DB' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUDB 98 " --> pdb=" O SERDB 94 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SERDB 99 " --> pdb=" O GLYDB 95 " (cutoff:3.500A) Proline residue: DB 108 - end of helix Processing helix chain 'DB' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILEDB 119 " --> pdb=" O ALADB 115 " (cutoff:3.500A) Processing helix chain 'DB' and resid 145 through 152 Processing helix chain 'DB' and resid 158 through 174 Processing helix chain 'EB' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYSEB 30 " --> pdb=" O ASPEB 26 " (cutoff:3.500A) Processing helix chain 'EB' and resid 44 through 106 Processing helix chain 'EB' and resid 107 through 140 removed outlier: 3.916A pdb=" N THREB 140 " --> pdb=" O METEB 136 " (cutoff:3.500A) Processing helix chain 'EB' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALAEB 160 " --> pdb=" O METEB 156 " (cutoff:3.500A) Processing helix chain 'EB' and resid 188 through 199 Processing helix chain 'FB' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSFB 38 " --> pdb=" O GLNFB 34 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLUFB 39 " --> pdb=" O LYSFB 35 " (cutoff:3.500A) Processing helix chain 'FB' and resid 49 through 82 Processing helix chain 'FB' and resid 82 through 89 Processing helix chain 'FB' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUFB 98 " --> pdb=" O SERFB 94 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SERFB 99 " --> pdb=" O GLYFB 95 " (cutoff:3.500A) Proline residue: FB 108 - end of helix Processing helix chain 'FB' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILEFB 119 " --> pdb=" O ALAFB 115 " (cutoff:3.500A) Processing helix chain 'FB' and resid 145 through 152 Processing helix chain 'FB' and resid 158 through 174 Processing helix chain 'GB' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYSGB 30 " --> pdb=" O ASPGB 26 " (cutoff:3.500A) Processing helix chain 'GB' and resid 44 through 106 Processing helix chain 'GB' and resid 107 through 140 removed outlier: 3.917A pdb=" N THRGB 140 " --> pdb=" O METGB 136 " (cutoff:3.500A) Processing helix chain 'GB' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALAGB 160 " --> pdb=" O METGB 156 " (cutoff:3.500A) Processing helix chain 'GB' and resid 188 through 199 Processing helix chain 'HB' and resid 7 through 47 removed outlier: 3.947A pdb=" N LYSHB 38 " --> pdb=" O GLNHB 34 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLUHB 39 " --> pdb=" O LYSHB 35 " (cutoff:3.500A) Processing helix chain 'HB' and resid 49 through 82 Processing helix chain 'HB' and resid 82 through 89 Processing helix chain 'HB' and resid 93 through 110 removed outlier: 4.531A pdb=" N GLUHB 98 " --> pdb=" O SERHB 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERHB 99 " --> pdb=" O GLYHB 95 " (cutoff:3.500A) Proline residue: HB 108 - end of helix Processing helix chain 'HB' and resid 115 through 128 removed outlier: 4.324A pdb=" N ILEHB 119 " --> pdb=" O ALAHB 115 " (cutoff:3.500A) Processing helix chain 'HB' and resid 145 through 152 Processing helix chain 'HB' and resid 158 through 174 Processing helix chain 'IB' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYSIB 30 " --> pdb=" O ASPIB 26 " (cutoff:3.500A) Processing helix chain 'IB' and resid 44 through 106 Processing helix chain 'IB' and resid 107 through 140 removed outlier: 3.917A pdb=" N THRIB 140 " --> pdb=" O METIB 136 " (cutoff:3.500A) Processing helix chain 'IB' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALAIB 160 " --> pdb=" O METIB 156 " (cutoff:3.500A) Processing helix chain 'IB' and resid 188 through 199 Processing helix chain 'JB' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSJB 38 " --> pdb=" O GLNJB 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUJB 39 " --> pdb=" O LYSJB 35 " (cutoff:3.500A) Processing helix chain 'JB' and resid 49 through 82 Processing helix chain 'JB' and resid 82 through 89 Processing helix chain 'JB' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUJB 98 " --> pdb=" O SERJB 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERJB 99 " --> pdb=" O GLYJB 95 " (cutoff:3.500A) Proline residue: JB 108 - end of helix Processing helix chain 'JB' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILEJB 119 " --> pdb=" O ALAJB 115 " (cutoff:3.500A) Processing helix chain 'JB' and resid 145 through 152 Processing helix chain 'JB' and resid 158 through 174 Processing helix chain 'KB' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYSKB 30 " --> pdb=" O ASPKB 26 " (cutoff:3.500A) Processing helix chain 'KB' and resid 44 through 106 Processing helix chain 'KB' and resid 107 through 140 removed outlier: 3.916A pdb=" N THRKB 140 " --> pdb=" O METKB 136 " (cutoff:3.500A) Processing helix chain 'KB' and resid 145 through 161 removed outlier: 3.721A pdb=" N ALAKB 160 " --> pdb=" O METKB 156 " (cutoff:3.500A) Processing helix chain 'KB' and resid 188 through 199 Processing helix chain 'LB' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSLB 38 " --> pdb=" O GLNLB 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLULB 39 " --> pdb=" O LYSLB 35 " (cutoff:3.500A) Processing helix chain 'LB' and resid 49 through 82 Processing helix chain 'LB' and resid 82 through 89 Processing helix chain 'LB' and resid 93 through 110 removed outlier: 4.529A pdb=" N GLULB 98 " --> pdb=" O SERLB 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERLB 99 " --> pdb=" O GLYLB 95 " (cutoff:3.500A) Proline residue: LB 108 - end of helix Processing helix chain 'LB' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILELB 119 " --> pdb=" O ALALB 115 " (cutoff:3.500A) Processing helix chain 'LB' and resid 145 through 152 Processing helix chain 'LB' and resid 158 through 174 Processing helix chain 'MB' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYSMB 30 " --> pdb=" O ASPMB 26 " (cutoff:3.500A) Processing helix chain 'MB' and resid 44 through 106 Processing helix chain 'MB' and resid 107 through 140 removed outlier: 3.916A pdb=" N THRMB 140 " --> pdb=" O METMB 136 " (cutoff:3.500A) Processing helix chain 'MB' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALAMB 160 " --> pdb=" O METMB 156 " (cutoff:3.500A) Processing helix chain 'MB' and resid 188 through 199 Processing helix chain 'NB' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSNB 38 " --> pdb=" O GLNNB 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUNB 39 " --> pdb=" O LYSNB 35 " (cutoff:3.500A) Processing helix chain 'NB' and resid 49 through 82 Processing helix chain 'NB' and resid 82 through 89 Processing helix chain 'NB' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUNB 98 " --> pdb=" O SERNB 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERNB 99 " --> pdb=" O GLYNB 95 " (cutoff:3.500A) Proline residue: NB 108 - end of helix Processing helix chain 'NB' and resid 115 through 128 removed outlier: 4.322A pdb=" N ILENB 119 " --> pdb=" O ALANB 115 " (cutoff:3.500A) Processing helix chain 'NB' and resid 145 through 152 Processing helix chain 'NB' and resid 158 through 174 Processing helix chain 'OB' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYSOB 30 " --> pdb=" O ASPOB 26 " (cutoff:3.500A) Processing helix chain 'OB' and resid 44 through 106 Processing helix chain 'OB' and resid 107 through 140 removed outlier: 3.917A pdb=" N THROB 140 " --> pdb=" O METOB 136 " (cutoff:3.500A) Processing helix chain 'OB' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALAOB 160 " --> pdb=" O METOB 156 " (cutoff:3.500A) Processing helix chain 'OB' and resid 188 through 199 Processing helix chain 'PB' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSPB 38 " --> pdb=" O GLNPB 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUPB 39 " --> pdb=" O LYSPB 35 " (cutoff:3.500A) Processing helix chain 'PB' and resid 49 through 82 Processing helix chain 'PB' and resid 82 through 89 Processing helix chain 'PB' and resid 93 through 110 removed outlier: 4.531A pdb=" N GLUPB 98 " --> pdb=" O SERPB 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERPB 99 " --> pdb=" O GLYPB 95 " (cutoff:3.500A) Proline residue: PB 108 - end of helix Processing helix chain 'PB' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILEPB 119 " --> pdb=" O ALAPB 115 " (cutoff:3.500A) Processing helix chain 'PB' and resid 145 through 152 Processing helix chain 'PB' and resid 158 through 174 Processing helix chain 'QB' and resid 5 through 43 removed outlier: 3.624A pdb=" N LYSQB 30 " --> pdb=" O ASPQB 26 " (cutoff:3.500A) Processing helix chain 'QB' and resid 44 through 106 Processing helix chain 'QB' and resid 107 through 140 removed outlier: 3.917A pdb=" N THRQB 140 " --> pdb=" O METQB 136 " (cutoff:3.500A) Processing helix chain 'QB' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALAQB 160 " --> pdb=" O METQB 156 " (cutoff:3.500A) Processing helix chain 'QB' and resid 188 through 199 Processing helix chain 'RB' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSRB 38 " --> pdb=" O GLNRB 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLURB 39 " --> pdb=" O LYSRB 35 " (cutoff:3.500A) Processing helix chain 'RB' and resid 49 through 82 Processing helix chain 'RB' and resid 82 through 89 Processing helix chain 'RB' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLURB 98 " --> pdb=" O SERRB 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERRB 99 " --> pdb=" O GLYRB 95 " (cutoff:3.500A) Proline residue: RB 108 - end of helix Processing helix chain 'RB' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILERB 119 " --> pdb=" O ALARB 115 " (cutoff:3.500A) Processing helix chain 'RB' and resid 145 through 152 Processing helix chain 'RB' and resid 158 through 174 Processing helix chain 'SB' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYSSB 30 " --> pdb=" O ASPSB 26 " (cutoff:3.500A) Processing helix chain 'SB' and resid 44 through 106 Processing helix chain 'SB' and resid 107 through 140 removed outlier: 3.916A pdb=" N THRSB 140 " --> pdb=" O METSB 136 " (cutoff:3.500A) Processing helix chain 'SB' and resid 145 through 161 removed outlier: 3.722A pdb=" N ALASB 160 " --> pdb=" O METSB 156 " (cutoff:3.500A) Processing helix chain 'SB' and resid 188 through 199 Processing helix chain 'TB' and resid 7 through 47 removed outlier: 3.948A pdb=" N LYSTB 38 " --> pdb=" O GLNTB 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLUTB 39 " --> pdb=" O LYSTB 35 " (cutoff:3.500A) Processing helix chain 'TB' and resid 49 through 82 Processing helix chain 'TB' and resid 82 through 89 Processing helix chain 'TB' and resid 93 through 110 removed outlier: 4.530A pdb=" N GLUTB 98 " --> pdb=" O SERTB 94 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SERTB 99 " --> pdb=" O GLYTB 95 " (cutoff:3.500A) Proline residue: TB 108 - end of helix Processing helix chain 'TB' and resid 115 through 128 removed outlier: 4.323A pdb=" N ILETB 119 " --> pdb=" O ALATB 115 " (cutoff:3.500A) Processing helix chain 'TB' and resid 145 through 152 Processing helix chain 'TB' and resid 158 through 174 Processing helix chain 'UB' and resid 5 through 43 removed outlier: 3.625A pdb=" N LYSUB 30 " --> pdb=" O ASPUB 26 " (cutoff:3.500A) Processing helix chain 'UB' and resid 44 through 106 Processing helix chain 'UB' and resid 107 through 140 removed outlier: 3.917A pdb=" N THRUB 140 " --> pdb=" O METUB 136 " (cutoff:3.500A) Processing helix chain 'UB' and resid 145 through 161 removed outlier: 3.723A pdb=" N ALAUB 160 " --> pdb=" O METUB 156 " (cutoff:3.500A) Processing helix chain 'UB' and resid 188 through 199 8856 hydrogen bonds defined for protein. 26568 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: 34.00 Time building geometry restraints manager: 34.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 31939 1.34 - 1.46: 8722 1.46 - 1.57: 56287 1.57 - 1.69: 0 1.69 - 1.81: 1188 Bond restraints: 98136 Sorted by residual: bond pdb=" CB GLN R 61 " pdb=" CG GLN R 61 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.15e+00 bond pdb=" CB GLN L 61 " pdb=" CG GLN L 61 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.15e+00 bond pdb=" CG LEU D 125 " pdb=" CD2 LEU D 125 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.13e+00 bond pdb=" CB GLNAB 61 " pdb=" CG GLNAB 61 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CB GLNOB 61 " pdb=" CG GLNOB 61 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.13e+00 ... (remaining 98131 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.39: 1692 106.39 - 113.28: 55770 113.28 - 120.17: 37525 120.17 - 127.06: 36089 127.06 - 133.95: 432 Bond angle restraints: 131508 Sorted by residual: angle pdb=" CG1 VALFB 114 " pdb=" CB VALFB 114 " pdb=" CG2 VALFB 114 " ideal model delta sigma weight residual 110.80 104.43 6.37 2.20e+00 2.07e-01 8.38e+00 angle pdb=" CG1 VAL S 114 " pdb=" CB VAL S 114 " pdb=" CG2 VAL S 114 " ideal model delta sigma weight residual 110.80 104.45 6.35 2.20e+00 2.07e-01 8.34e+00 angle pdb=" CG1 VALLA 114 " pdb=" CB VALLA 114 " pdb=" CG2 VALLA 114 " ideal model delta sigma weight residual 110.80 104.46 6.34 2.20e+00 2.07e-01 8.31e+00 angle pdb=" CG1 VAL Z 114 " pdb=" CB VAL Z 114 " pdb=" CG2 VAL Z 114 " ideal model delta sigma weight residual 110.80 104.46 6.34 2.20e+00 2.07e-01 8.30e+00 angle pdb=" CG1 VALRB 114 " pdb=" CB VALRB 114 " pdb=" CG2 VALRB 114 " ideal model delta sigma weight residual 110.80 104.46 6.34 2.20e+00 2.07e-01 8.29e+00 ... (remaining 131503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.02: 58068 14.02 - 28.04: 2938 28.04 - 42.06: 1130 42.06 - 56.09: 216 56.09 - 70.11: 72 Dihedral angle restraints: 62424 sinusoidal: 26100 harmonic: 36324 Sorted by residual: dihedral pdb=" N TYRNB 165 " pdb=" CA TYRNB 165 " pdb=" CB TYRNB 165 " pdb=" CG TYRNB 165 " ideal model delta sinusoidal sigma weight residual -180.00 -124.00 -56.00 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" N TYRFA 165 " pdb=" CA TYRFA 165 " pdb=" CB TYRFA 165 " pdb=" CG TYRFA 165 " ideal model delta sinusoidal sigma weight residual -180.00 -124.00 -56.00 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" N TYR I 165 " pdb=" CA TYR I 165 " pdb=" CB TYR I 165 " pdb=" CG TYR I 165 " ideal model delta sinusoidal sigma weight residual -180.00 -124.01 -55.99 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 62421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 8898 0.038 - 0.076: 4844 0.076 - 0.114: 1202 0.114 - 0.152: 356 0.152 - 0.190: 72 Chirality restraints: 15372 Sorted by residual: chirality pdb=" CB THRMA 141 " pdb=" CA THRMA 141 " pdb=" OG1 THRMA 141 " pdb=" CG2 THRMA 141 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CB THR J 141 " pdb=" CA THR J 141 " pdb=" OG1 THR J 141 " pdb=" CG2 THR J 141 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CB THR R 141 " pdb=" CA THR R 141 " pdb=" OG1 THR R 141 " pdb=" CG2 THR R 141 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 15369 not shown) Planarity restraints: 16776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEGB 65 " -0.013 2.00e-02 2.50e+03 1.54e-02 4.14e+00 pdb=" CG PHEGB 65 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHEGB 65 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHEGB 65 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHEGB 65 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEGB 65 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHEGB 65 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEIA 65 " -0.013 2.00e-02 2.50e+03 1.53e-02 4.12e+00 pdb=" CG PHEIA 65 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHEIA 65 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHEIA 65 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHEIA 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEIA 65 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHEIA 65 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEUB 65 " 0.013 2.00e-02 2.50e+03 1.53e-02 4.10e+00 pdb=" CG PHEUB 65 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHEUB 65 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHEUB 65 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHEUB 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEUB 65 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHEUB 65 " -0.002 2.00e-02 2.50e+03 ... (remaining 16773 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 7050 2.74 - 3.28: 97328 3.28 - 3.82: 166389 3.82 - 4.36: 190653 4.36 - 4.90: 335125 Nonbonded interactions: 796545 Sorted by model distance: nonbonded pdb=" OH TYRPA 165 " pdb=" NH1 ARGQA 196 " model vdw 2.201 2.520 nonbonded pdb=" OH TYR S 165 " pdb=" NH1 ARG T 196 " model vdw 2.201 2.520 nonbonded pdb=" OH TYR Q 165 " pdb=" NH1 ARG R 196 " model vdw 2.201 2.520 nonbonded pdb=" OH TYRTB 165 " pdb=" NH1 ARGUB 196 " model vdw 2.201 2.520 nonbonded pdb=" OH TYRDB 165 " pdb=" NH1 ARGEB 196 " model vdw 2.201 2.520 ... (remaining 796540 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' selection = chain 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'JA' selection = chain 'JB' selection = chain 'K' selection = chain 'LA' selection = chain 'LB' selection = chain 'M' selection = chain 'NA' selection = chain 'NB' selection = chain 'O' selection = chain 'PA' selection = chain 'PB' selection = chain 'Q' selection = chain 'RA' selection = chain 'RB' selection = chain 'S' selection = chain 'TA' selection = chain 'TB' selection = chain 'V' selection = chain 'VA' selection = chain 'X' selection = chain 'XA' selection = chain 'Z' selection = chain 'ZA' } ncs_group { reference = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'KA' selection = chain 'KB' selection = chain 'L' selection = chain 'MA' selection = chain 'MB' selection = chain 'N' selection = chain 'OA' selection = chain 'OB' selection = chain 'P' selection = chain 'QA' selection = chain 'QB' selection = chain 'R' selection = chain 'SA' selection = chain 'SB' selection = chain 'T' selection = chain 'UA' selection = chain 'UB' selection = chain 'W' selection = chain 'WA' selection = chain 'Y' selection = chain 'YA' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 648 5.16 5 C 60948 2.51 5 N 17244 2.21 5 O 18432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 0.060 Extract box with map and model: 19.660 Check model and map are aligned: 1.170 Convert atoms to be neutral: 0.650 Process input model: 189.970 Find NCS groups from input model: 5.770 Set up NCS constraints: 1.360 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 232.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 0.048 98136 Z= 0.378 Angle : 0.889 9.869 131508 Z= 0.472 Chirality : 0.049 0.190 15372 Planarity : 0.006 0.047 16776 Dihedral : 10.624 70.107 38520 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.06), residues: 11988 helix: -0.77 (0.04), residues: 10764 sheet: None (None), residues: 0 loop : -1.41 (0.15), residues: 1224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4346 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 4310 time to evaluate : 9.393 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 4331 average time/residue: 1.8740 time to fit residues: 10687.8088 Evaluate side-chains 2606 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 2586 time to evaluate : 9.457 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 10 residues processed: 10 average time/residue: 1.0178 time to fit residues: 29.0167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1188 random chunks: chunk 1003 optimal weight: 8.9990 chunk 900 optimal weight: 0.9980 chunk 499 optimal weight: 5.9990 chunk 307 optimal weight: 7.9990 chunk 607 optimal weight: 9.9990 chunk 481 optimal weight: 6.9990 chunk 931 optimal weight: 0.7980 chunk 360 optimal weight: 3.9990 chunk 566 optimal weight: 2.9990 chunk 693 optimal weight: 9.9990 chunk 1078 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 34 GLN T 61 GLN T 120 HIS T 146 GLN T 148 GLN B 130 GLN C 20 ASN C 34 GLN D 61 GLN D 121 GLN D 146 GLN D 148 GLN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS G 34 GLN H 120 HIS H 146 GLN H 154 GLN J 61 GLN J 130 GLN ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN N 130 GLN R 41 GLN R 121 GLN R 131 GLN V 14 ASN V 20 ASN V 34 GLN W 131 GLN W 147 ASN Y 131 GLN Z 34 GLN AA 120 HIS AA 121 GLN AA 148 GLN AA 154 GLN BA 20 ASN CA 61 GLN CA 120 HIS CA 146 GLN CA 148 GLN DA 34 GLN EA 120 HIS ** EA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 34 GLN ** GA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 61 GLN IA 120 HIS IA 146 GLN IA 148 GLN JA 34 GLN KA 61 GLN KA 146 GLN KA 148 GLN LA 34 GLN MA 61 GLN MA 130 GLN MA 148 GLN NA 150 HIS ** NA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 120 HIS OA 130 GLN OA 131 GLN ** OA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 148 GLN OA 154 GLN QA 41 GLN QA 120 HIS RA 34 GLN SA 130 GLN SA 146 GLN SA 148 GLN ** TA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 146 GLN UA 148 GLN WA 130 GLN YA 61 GLN YA 120 HIS ZA 20 ASN AB 130 GLN AB 147 ASN BB 34 GLN CB 61 GLN CB 130 GLN CB 146 GLN DB 14 ASN DB 20 ASN DB 34 GLN EB 121 GLN FB 34 GLN GB 128 GLN GB 131 GLN HB 34 GLN ** HB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IB 120 HIS IB 121 GLN IB 130 GLN IB 148 GLN JB 34 GLN MB 120 HIS ** MB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 34 GLN QB 130 GLN QB 154 GLN SB 61 GLN SB 120 HIS SB 121 GLN SB 146 GLN UB 121 GLN UB 146 GLN UB 148 GLN Total number of N/Q/H flips: 103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 98136 Z= 0.192 Angle : 0.512 6.593 131508 Z= 0.271 Chirality : 0.035 0.139 15372 Planarity : 0.004 0.053 16776 Dihedral : 3.629 14.294 13212 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer Outliers : 6.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.07), residues: 11988 helix: 1.56 (0.04), residues: 10800 sheet: None (None), residues: 0 loop : -1.16 (0.15), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3369 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 644 poor density : 2725 time to evaluate : 9.546 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 outliers start: 644 outliers final: 125 residues processed: 3051 average time/residue: 1.7047 time to fit residues: 7080.8387 Evaluate side-chains 2594 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 2469 time to evaluate : 9.369 Switching outliers to nearest non-outliers outliers start: 125 outliers final: 51 residues processed: 78 average time/residue: 1.0802 time to fit residues: 145.2569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1188 random chunks: chunk 599 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 897 optimal weight: 5.9990 chunk 734 optimal weight: 6.9990 chunk 297 optimal weight: 9.9990 chunk 1080 optimal weight: 0.9990 chunk 1167 optimal weight: 20.0000 chunk 962 optimal weight: 9.9990 chunk 1071 optimal weight: 3.9990 chunk 368 optimal weight: 9.9990 chunk 867 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 34 GLN T 61 GLN T 146 GLN B 147 ASN D 61 GLN D 147 ASN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS F 121 GLN G 34 GLN I 172 ASN J 147 ASN L 61 GLN L 146 GLN L 154 GLN N 121 GLN O 34 GLN P 41 GLN ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 147 ASN Y 41 GLN Z 34 GLN ** AA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 148 GLN AA 154 GLN ** BA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 34 GLN EA 154 GLN FA 34 GLN GA 147 ASN HA 14 ASN HA 34 GLN IA 61 GLN IA 120 HIS IA 146 GLN KA 61 GLN KA 121 GLN MA 61 GLN MA 121 GLN MA 147 ASN ** NA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 120 HIS OA 154 GLN QA 120 HIS RA 14 ASN RA 34 GLN SA 121 GLN TA 34 GLN ** TA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 121 GLN UA 146 GLN ** VA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** WA 147 ASN YA 61 GLN YA 121 GLN YA 154 GLN AB 41 GLN AB 146 GLN BB 34 GLN CB 146 GLN DB 34 GLN ** DB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 34 GLN ** FB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IB 120 HIS KB 147 ASN ** LB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MB 120 HIS MB 146 GLN ** NB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** QB 154 GLN SB 61 GLN SB 146 GLN TB 34 GLN ** UB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UB 146 GLN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 98136 Z= 0.261 Angle : 0.538 11.092 131508 Z= 0.277 Chirality : 0.037 0.127 15372 Planarity : 0.004 0.058 16776 Dihedral : 3.466 11.953 13212 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 5.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.07), residues: 11988 helix: 2.39 (0.05), residues: 10800 sheet: None (None), residues: 0 loop : -0.96 (0.16), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3096 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 556 poor density : 2540 time to evaluate : 9.699 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 outliers start: 556 outliers final: 189 residues processed: 2782 average time/residue: 1.7389 time to fit residues: 6563.5574 Evaluate side-chains 2463 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 2274 time to evaluate : 9.556 Switching outliers to nearest non-outliers outliers start: 189 outliers final: 84 residues processed: 107 average time/residue: 1.1863 time to fit residues: 205.8368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1188 random chunks: chunk 1067 optimal weight: 2.9990 chunk 812 optimal weight: 10.0000 chunk 560 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 515 optimal weight: 5.9990 chunk 725 optimal weight: 20.0000 chunk 1084 optimal weight: 0.9990 chunk 1148 optimal weight: 8.9990 chunk 566 optimal weight: 2.9990 chunk 1027 optimal weight: 0.9980 chunk 309 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 34 GLN T 121 GLN T 154 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN E 34 GLN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS G 34 GLN H 146 GLN H 147 ASN L 61 GLN N 121 GLN O 34 GLN Q 34 GLN ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 172 ASN W 41 GLN W 147 ASN Z 34 GLN AA 154 GLN ** BA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 34 GLN EA 120 HIS EA 121 GLN EA 147 ASN FA 34 GLN GA 146 GLN HA 34 GLN IA 120 HIS IA 146 GLN JA 34 GLN ** KA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KA 147 ASN ** NA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 146 GLN QA 41 GLN QA 120 HIS QA 121 GLN QA 131 GLN RA 34 GLN TA 34 GLN ** TA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 146 GLN UA 148 GLN VA 172 ASN ZA 34 GLN BB 34 GLN CB 147 ASN DB 34 GLN ** DB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 14 ASN FB 34 GLN ** FB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 121 GLN ** HB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IB 61 GLN IB 120 HIS IB 147 ASN KB 147 ASN LB 34 GLN LB 172 ASN MB 120 HIS NB 34 GLN ** NB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OB 121 GLN OB 146 GLN PB 34 GLN QB 130 GLN ** QB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RB 34 GLN SB 147 ASN TB 34 GLN ** UB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UB 146 GLN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 98136 Z= 0.220 Angle : 0.518 9.703 131508 Z= 0.262 Chirality : 0.036 0.129 15372 Planarity : 0.004 0.054 16776 Dihedral : 3.337 11.229 13212 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 4.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.07), residues: 11988 helix: 2.88 (0.04), residues: 10584 sheet: None (None), residues: 0 loop : -0.90 (0.14), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2862 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 507 poor density : 2355 time to evaluate : 9.791 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 outliers start: 507 outliers final: 223 residues processed: 2580 average time/residue: 1.7046 time to fit residues: 5986.2367 Evaluate side-chains 2474 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 2251 time to evaluate : 9.457 Switching outliers to nearest non-outliers outliers start: 223 outliers final: 93 residues processed: 135 average time/residue: 1.1743 time to fit residues: 253.3051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1188 random chunks: chunk 956 optimal weight: 20.0000 chunk 651 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 855 optimal weight: 8.9990 chunk 473 optimal weight: 9.9990 chunk 979 optimal weight: 5.9990 chunk 793 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 586 optimal weight: 8.9990 chunk 1030 optimal weight: 5.9990 chunk 289 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 34 GLN ** T 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN C 34 GLN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS G 34 GLN H 146 GLN O 34 GLN Q 34 GLN ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 146 GLN Z 34 GLN ** AA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 147 ASN AA 148 GLN AA 154 GLN ** BA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 34 GLN EA 61 GLN ** EA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 34 GLN GA 147 ASN HA 34 GLN IA 41 GLN IA 120 HIS IA 146 GLN JA 34 GLN ** KA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 120 HIS NA 34 GLN ** NA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 120 HIS QA 148 GLN RA 34 GLN TA 34 GLN ** TA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 41 GLN UA 148 GLN BB 34 GLN DB 34 GLN ** DB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 34 GLN ** FB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IB 61 GLN IB 120 HIS IB 147 ASN JB 34 GLN KB 147 ASN MB 120 HIS NB 34 GLN ** NB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 34 GLN QB 146 GLN ** UB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UB 147 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 98136 Z= 0.199 Angle : 0.505 11.043 131508 Z= 0.255 Chirality : 0.035 0.119 15372 Planarity : 0.004 0.050 16776 Dihedral : 3.267 10.998 13212 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer Outliers : 4.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.15 (0.07), residues: 11988 helix: 3.14 (0.04), residues: 10584 sheet: None (None), residues: 0 loop : -0.78 (0.14), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2839 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 467 poor density : 2372 time to evaluate : 9.586 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 outliers start: 467 outliers final: 201 residues processed: 2570 average time/residue: 1.6834 time to fit residues: 5910.1416 Evaluate side-chains 2472 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 2271 time to evaluate : 9.420 Switching outliers to nearest non-outliers outliers start: 201 outliers final: 88 residues processed: 115 average time/residue: 1.2366 time to fit residues: 225.4389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1188 random chunks: chunk 386 optimal weight: 6.9990 chunk 1034 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 674 optimal weight: 10.0000 chunk 283 optimal weight: 9.9990 chunk 1149 optimal weight: 0.8980 chunk 954 optimal weight: 8.9990 chunk 532 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 380 optimal weight: 3.9990 chunk 603 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 34 GLN ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN E 34 GLN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN H 146 GLN H 147 ASN O 34 GLN P 41 GLN Q 34 GLN R 121 GLN W 131 GLN W 146 GLN W 147 ASN Y 41 GLN Y 131 GLN Z 34 GLN ** BA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 34 GLN ** EA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 34 GLN HA 34 GLN IA 120 HIS IA 146 GLN JA 34 GLN ** KA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 148 GLN NA 34 GLN ** NA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 41 GLN QA 120 HIS RA 34 GLN ** SA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 34 GLN ** TA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 131 GLN YA 41 GLN YA 147 ASN ZA 34 GLN AB 41 GLN BB 34 GLN DB 34 GLN ** DB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 34 GLN ** FB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IB 120 HIS KB 146 GLN KB 147 ASN MB 120 HIS NB 34 GLN ** NB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 34 GLN TB 34 GLN UB 121 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 98136 Z= 0.277 Angle : 0.552 11.192 131508 Z= 0.278 Chirality : 0.037 0.252 15372 Planarity : 0.004 0.050 16776 Dihedral : 3.319 11.479 13212 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer Outliers : 4.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.02 (0.07), residues: 11988 helix: 3.03 (0.04), residues: 10584 sheet: None (None), residues: 0 loop : -0.68 (0.14), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2768 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 441 poor density : 2327 time to evaluate : 9.715 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 outliers start: 441 outliers final: 211 residues processed: 2503 average time/residue: 1.6956 time to fit residues: 5787.4433 Evaluate side-chains 2426 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 2215 time to evaluate : 9.537 Switching outliers to nearest non-outliers outliers start: 211 outliers final: 106 residues processed: 106 average time/residue: 1.2060 time to fit residues: 205.4168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1188 random chunks: chunk 1108 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 654 optimal weight: 3.9990 chunk 839 optimal weight: 2.9990 chunk 650 optimal weight: 0.9990 chunk 967 optimal weight: 10.0000 chunk 641 optimal weight: 20.0000 chunk 1145 optimal weight: 5.9990 chunk 716 optimal weight: 5.9990 chunk 698 optimal weight: 3.9990 chunk 528 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 34 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN C 34 GLN D 146 GLN D 154 GLN E 34 GLN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN L 147 ASN O 34 GLN P 41 GLN P 131 GLN P 148 GLN Q 34 GLN W 146 GLN Y 41 GLN Y 131 GLN Z 34 GLN ** AA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 34 GLN ** EA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 147 ASN FA 34 GLN HA 34 GLN IA 41 GLN IA 120 HIS IA 146 GLN JA 34 GLN ** KA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 34 GLN NA 172 ASN QA 120 HIS RA 34 GLN TA 34 GLN ** TA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 34 GLN AB 41 GLN BB 34 GLN DB 34 GLN ** DB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 34 GLN ** FB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IB 120 HIS MB 120 HIS NB 34 GLN ** NB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 34 GLN TB 34 GLN UB 120 HIS UB 121 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 98136 Z= 0.259 Angle : 0.543 9.615 131508 Z= 0.275 Chirality : 0.037 0.222 15372 Planarity : 0.004 0.057 16776 Dihedral : 3.302 11.352 13212 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.07), residues: 11988 helix: 3.09 (0.04), residues: 10584 sheet: None (None), residues: 0 loop : -0.59 (0.14), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2681 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 407 poor density : 2274 time to evaluate : 9.791 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 outliers start: 407 outliers final: 224 residues processed: 2450 average time/residue: 1.6586 time to fit residues: 5569.3744 Evaluate side-chains 2461 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 2237 time to evaluate : 9.493 Switching outliers to nearest non-outliers outliers start: 224 outliers final: 114 residues processed: 114 average time/residue: 1.2391 time to fit residues: 224.1947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1188 random chunks: chunk 708 optimal weight: 4.9990 chunk 457 optimal weight: 2.9990 chunk 683 optimal weight: 3.9990 chunk 344 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 727 optimal weight: 3.9990 chunk 780 optimal weight: 4.9990 chunk 566 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 900 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 34 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 ASN O 34 GLN P 41 GLN Q 34 GLN W 146 GLN Z 34 GLN ** BA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 34 GLN HA 34 GLN IA 120 HIS IA 146 GLN JA 34 GLN KA 41 GLN ** KA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 120 HIS NA 34 GLN NA 150 HIS QA 120 HIS RA 34 GLN TA 34 GLN ** TA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** YA 147 ASN BB 34 GLN DB 34 GLN ** DB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 34 GLN ** FB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IB 120 HIS MB 120 HIS NB 34 GLN ** NB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 34 GLN SB 41 GLN UB 121 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 98136 Z= 0.251 Angle : 0.548 10.793 131508 Z= 0.278 Chirality : 0.036 0.226 15372 Planarity : 0.004 0.061 16776 Dihedral : 3.295 11.444 13212 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer Outliers : 3.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (0.07), residues: 11988 helix: 3.13 (0.04), residues: 10584 sheet: None (None), residues: 0 loop : -0.48 (0.15), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2669 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 379 poor density : 2290 time to evaluate : 9.870 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 outliers start: 379 outliers final: 217 residues processed: 2462 average time/residue: 1.6830 time to fit residues: 5676.0255 Evaluate side-chains 2432 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 2215 time to evaluate : 9.632 Switching outliers to nearest non-outliers outliers start: 217 outliers final: 119 residues processed: 100 average time/residue: 1.2223 time to fit residues: 196.7284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1188 random chunks: chunk 1041 optimal weight: 7.9990 chunk 1096 optimal weight: 3.9990 chunk 1000 optimal weight: 8.9990 chunk 1067 optimal weight: 7.9990 chunk 642 optimal weight: 5.9990 chunk 464 optimal weight: 5.9990 chunk 837 optimal weight: 8.9990 chunk 327 optimal weight: 3.9990 chunk 964 optimal weight: 3.9990 chunk 1009 optimal weight: 9.9990 chunk 1063 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 34 GLN T 146 GLN T 148 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN D 148 GLN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN L 147 ASN O 34 GLN P 41 GLN Q 34 GLN W 146 GLN W 148 GLN Y 41 GLN Y 131 GLN Z 34 GLN ** AA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 34 GLN HA 34 GLN IA 120 HIS IA 146 GLN JA 34 GLN ** KA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KA 146 GLN MA 120 HIS NA 34 GLN OA 148 GLN QA 120 HIS RA 34 GLN ** SA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 34 GLN ** TA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 41 GLN UA 146 GLN YA 41 GLN ZA 34 GLN AB 41 GLN AB 146 GLN BB 34 GLN DB 34 GLN ** DB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 34 GLN ** FB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IB 120 HIS MB 120 HIS NB 34 GLN ** NB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 34 GLN TB 34 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 98136 Z= 0.292 Angle : 0.576 10.989 131508 Z= 0.291 Chirality : 0.038 0.242 15372 Planarity : 0.004 0.063 16776 Dihedral : 3.348 11.864 13212 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.07), residues: 11988 helix: 3.02 (0.04), residues: 10584 sheet: None (None), residues: 0 loop : -0.40 (0.15), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2588 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 2266 time to evaluate : 9.711 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 outliers start: 322 outliers final: 189 residues processed: 2430 average time/residue: 1.7035 time to fit residues: 5670.0401 Evaluate side-chains 2404 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 2215 time to evaluate : 9.681 Switching outliers to nearest non-outliers outliers start: 189 outliers final: 119 residues processed: 73 average time/residue: 1.2613 time to fit residues: 150.8956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1188 random chunks: chunk 700 optimal weight: 5.9990 chunk 1128 optimal weight: 6.9990 chunk 688 optimal weight: 2.9990 chunk 535 optimal weight: 3.9990 chunk 784 optimal weight: 4.9990 chunk 1183 optimal weight: 5.9990 chunk 1089 optimal weight: 20.0000 chunk 942 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 727 optimal weight: 6.9990 chunk 577 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 34 GLN ** T 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 147 ASN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN C 34 GLN E 34 GLN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS G 34 GLN ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 ASN ** M 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN P 41 GLN Q 34 GLN W 146 GLN W 148 GLN Y 41 GLN Y 131 GLN Z 34 GLN ** BA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 34 GLN HA 34 GLN IA 120 HIS IA 146 GLN JA 34 GLN KA 41 GLN ** KA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 120 HIS NA 34 GLN ** PA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 120 HIS RA 34 GLN ** SA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 34 GLN ** TA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 34 GLN AB 146 GLN BB 34 GLN DB 34 GLN ** DB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 34 GLN ** FB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IB 120 HIS MB 120 HIS NB 34 GLN ** NB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 34 GLN ** QB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 41 GLN SB 154 GLN TB 34 GLN UB 120 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 98136 Z= 0.276 Angle : 0.581 12.012 131508 Z= 0.293 Chirality : 0.037 0.265 15372 Planarity : 0.004 0.064 16776 Dihedral : 3.349 11.591 13212 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.07), residues: 11988 helix: 3.03 (0.04), residues: 10584 sheet: None (None), residues: 0 loop : -0.32 (0.15), residues: 1404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23976 Ramachandran restraints generated. 11988 Oldfield, 0 Emsley, 11988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2486 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 2237 time to evaluate : 9.589 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 outliers start: 249 outliers final: 165 residues processed: 2373 average time/residue: 1.6995 time to fit residues: 5518.6085 Evaluate side-chains 2375 residues out of total 10584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 2210 time to evaluate : 9.371 Switching outliers to nearest non-outliers outliers start: 165 outliers final: 113 residues processed: 54 average time/residue: 1.2365 time to fit residues: 112.1435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1188 random chunks: chunk 748 optimal weight: 4.9990 chunk 1003 optimal weight: 9.9990 chunk 288 optimal weight: 7.9990 chunk 869 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 943 optimal weight: 10.0000 chunk 395 optimal weight: 20.0000 chunk 969 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 14 ASN S 34 GLN ** T 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN C 34 GLN E 34 GLN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN P 41 GLN Q 34 GLN W 146 GLN W 148 GLN Y 41 GLN Y 131 GLN Z 34 GLN ** BA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 146 GLN FA 34 GLN HA 34 GLN IA 120 HIS IA 146 GLN JA 34 GLN KA 121 GLN LA 14 ASN NA 34 GLN ** PA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 41 GLN QA 120 HIS ** QA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 34 GLN ** SA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 148 GLN TA 34 GLN ** TA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 14 ASN YA 41 GLN ZA 34 GLN AB 41 GLN AB 146 GLN BB 14 ASN BB 34 GLN DB 34 GLN ** DB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 34 GLN ** FB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IB 120 HIS MB 120 HIS NB 34 GLN ** NB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OB 121 GLN ** OB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 34 GLN ** QB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RB 14 ASN TB 34 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116478 restraints weight = 116460.048| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.47 r_work: 0.3279 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 98136 Z= 0.359 Angle : 0.619 13.043 131508 Z= 0.313 Chirality : 0.040 0.249 15372 Planarity : 0.004 0.064 16776 Dihedral : 3.451 12.403 13212 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.07), residues: 11988 helix: 2.83 (0.04), residues: 10584 sheet: None (None), residues: 0 loop : -0.29 (0.15), residues: 1404 =============================================================================== Job complete usr+sys time: 73851.36 seconds wall clock time: 1264 minutes 55.51 seconds (75895.51 seconds total)