Starting phenix.real_space_refine on Wed Apr 17 16:54:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5m_31727/04_2024/7v5m_31727.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5m_31727/04_2024/7v5m_31727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5m_31727/04_2024/7v5m_31727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5m_31727/04_2024/7v5m_31727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5m_31727/04_2024/7v5m_31727.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5m_31727/04_2024/7v5m_31727.pdb" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 280 5.16 5 C 28992 2.51 5 N 8010 2.21 5 O 8058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 88": "NH1" <-> "NH2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "G TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 79": "NH1" <-> "NH2" Residue "K TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 86": "NH1" <-> "NH2" Residue "K TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "L PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 158": "NH1" <-> "NH2" Residue "L ARG 186": "NH1" <-> "NH2" Residue "M PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "M PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 173": "NH1" <-> "NH2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "N TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 88": "NH1" <-> "NH2" Residue "O TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 213": "NH1" <-> "NH2" Residue "S PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 101": "NH1" <-> "NH2" Residue "U TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 143": "NH1" <-> "NH2" Residue "X ARG 25": "NH1" <-> "NH2" Residue "X ARG 69": "NH1" <-> "NH2" Residue "X ARG 79": "NH1" <-> "NH2" Residue "Y TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 153": "NH1" <-> "NH2" Residue "Z PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 158": "NH1" <-> "NH2" Residue "Z ARG 186": "NH1" <-> "NH2" Residue "a ARG 99": "NH1" <-> "NH2" Residue "a PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 173": "NH1" <-> "NH2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "b TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 45340 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1734 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1786 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "D" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1633 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1659 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "F" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1704 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1760 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 77 Chain: "H" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1465 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "I" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1576 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "J" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1534 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "K" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1506 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1500 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1583 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 55 Chain: "N" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1568 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "O" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1734 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "P" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "Q" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1786 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "R" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1633 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "S" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1659 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "T" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1704 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "U" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1760 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 77 Chain: "V" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1465 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "W" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1576 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "X" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1534 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "Y" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1506 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "Z" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1500 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "a" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1583 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 55 Chain: "b" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1568 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 23.01, per 1000 atoms: 0.51 Number of scatterers: 45340 At special positions: 0 Unit cell: (192.428, 156.842, 131.8, 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 280 16.00 O 8058 8.00 N 8010 7.00 C 28992 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: 15.62 Conformation dependent library (CDL) restraints added in 9.0 seconds 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11416 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 70 sheets defined 38.8% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 removed outlier: 3.863A pdb=" N ASP A 10 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG A 11 " --> pdb=" O GLY A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.869A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 36 Processing helix chain 'A' and resid 83 through 106 removed outlier: 3.848A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.712A pdb=" N CYS A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.506A pdb=" N SER A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 189 removed outlier: 4.346A pdb=" N TRP A 189 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 207 removed outlier: 3.740A pdb=" N THR A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 removed outlier: 3.580A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 30 removed outlier: 3.798A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 27 " --> pdb=" O TYR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 101 removed outlier: 3.532A pdb=" N ARG B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.526A pdb=" N ARG B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.517A pdb=" N THR B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 4.046A pdb=" N HIS B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 removed outlier: 3.961A pdb=" N ILE B 207 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 removed outlier: 3.592A pdb=" N ASP B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.649A pdb=" N GLU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.878A pdb=" N ASN C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 removed outlier: 3.550A pdb=" N VAL C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 176 Processing helix chain 'C' and resid 185 through 200 removed outlier: 4.055A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 247 removed outlier: 3.698A pdb=" N LEU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 removed outlier: 3.633A pdb=" N VAL D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 99 removed outlier: 3.673A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.800A pdb=" N THR D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.663A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 removed outlier: 3.738A pdb=" N VAL D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 232 removed outlier: 3.765A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.576A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 85 through 104 Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 173 through 185 removed outlier: 6.819A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E 184 " --> pdb=" O SER E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 removed outlier: 3.532A pdb=" N LEU E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.725A pdb=" N GLU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 29 removed outlier: 3.503A pdb=" N GLU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 99 removed outlier: 3.700A pdb=" N PHE F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.816A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix removed outlier: 3.504A pdb=" N ARG F 122 " --> pdb=" O ILE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 176 Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.701A pdb=" N VAL F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'G' and resid 6 through 10 removed outlier: 4.305A pdb=" N SER G 10 " --> pdb=" O TYR G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 32 removed outlier: 3.529A pdb=" N LYS G 28 " --> pdb=" O GLU G 24 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA G 29 " --> pdb=" O TYR G 25 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU G 31 " --> pdb=" O MET G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 103 removed outlier: 3.641A pdb=" N SER G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE G 98 " --> pdb=" O GLU G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.573A pdb=" N ASP G 113 " --> pdb=" O LYS G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 removed outlier: 4.174A pdb=" N ALA G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS G 173 " --> pdb=" O ARG G 169 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS G 178 " --> pdb=" O THR G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 3.993A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 244 removed outlier: 3.566A pdb=" N SER G 242 " --> pdb=" O TYR G 238 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS G 244 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 removed outlier: 3.564A pdb=" N ALA H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.574A pdb=" N ALA H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU H 82 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 134 removed outlier: 3.527A pdb=" N TYR H 134 " --> pdb=" O GLY H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 142 removed outlier: 3.519A pdb=" N ALA H 141 " --> pdb=" O GLY H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 167 removed outlier: 3.509A pdb=" N GLN H 154 " --> pdb=" O GLU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.879A pdb=" N ILE H 194 " --> pdb=" O GLY H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 71 removed outlier: 3.697A pdb=" N LEU I 58 " --> pdb=" O MET I 54 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 90 Processing helix chain 'I' and resid 130 through 142 removed outlier: 4.043A pdb=" N ALA I 136 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE I 138 " --> pdb=" O ALA I 134 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 164 removed outlier: 3.531A pdb=" N GLY I 162 " --> pdb=" O ALA I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 5 Processing helix chain 'J' and resid 55 through 78 Processing helix chain 'J' and resid 82 through 97 removed outlier: 3.846A pdb=" N SER J 88 " --> pdb=" O TYR J 84 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 removed outlier: 3.591A pdb=" N TYR J 146 " --> pdb=" O ALA J 142 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY J 147 " --> pdb=" O GLU J 143 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET J 148 " --> pdb=" O GLN J 144 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU J 150 " --> pdb=" O TYR J 146 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU J 152 " --> pdb=" O MET J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 175 removed outlier: 3.555A pdb=" N GLU J 164 " --> pdb=" O ASP J 160 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 72 removed outlier: 3.743A pdb=" N GLN K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU K 58 " --> pdb=" O VAL K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 90 removed outlier: 3.852A pdb=" N ASN K 87 " --> pdb=" O PHE K 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU K 88 " --> pdb=" O THR K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 143 removed outlier: 4.628A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 170 removed outlier: 3.538A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU K 167 " --> pdb=" O CYS K 163 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN K 168 " --> pdb=" O LEU K 164 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS K 169 " --> pdb=" O GLU K 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 71 removed outlier: 3.600A pdb=" N GLU L 56 " --> pdb=" O CYS L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 88 removed outlier: 3.508A pdb=" N VAL L 87 " --> pdb=" O LEU L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 4.250A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG L 141 " --> pdb=" O GLY L 137 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY L 142 " --> pdb=" O VAL L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 removed outlier: 3.623A pdb=" N ASP L 154 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU L 155 " --> pdb=" O GLN L 151 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE L 160 " --> pdb=" O ALA L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 199 removed outlier: 4.219A pdb=" N GLU L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 80 removed outlier: 3.787A pdb=" N LYS M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET M 74 " --> pdb=" O ALA M 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.553A pdb=" N THR M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 153 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 167 through 186 removed outlier: 3.521A pdb=" N MET M 172 " --> pdb=" O LEU M 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE M 180 " --> pdb=" O LYS M 176 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER M 181 " --> pdb=" O ASP M 177 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG M 185 " --> pdb=" O SER M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 78 removed outlier: 3.538A pdb=" N GLN N 69 " --> pdb=" O GLN N 65 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET N 70 " --> pdb=" O VAL N 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL N 71 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE N 72 " --> pdb=" O GLY N 68 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 removed outlier: 3.504A pdb=" N ARG N 99 " --> pdb=" O ALA N 95 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG N 100 " --> pdb=" O MET N 96 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS N 102 " --> pdb=" O SER N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 removed outlier: 3.926A pdb=" N LYS N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 180 removed outlier: 3.570A pdb=" N ARG N 179 " --> pdb=" O VAL N 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 12 removed outlier: 3.864A pdb=" N ASP O 10 " --> pdb=" O ALA O 7 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG O 11 " --> pdb=" O GLY O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 31 removed outlier: 3.869A pdb=" N LYS O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 36 Processing helix chain 'O' and resid 83 through 106 removed outlier: 3.847A pdb=" N SER O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 128 removed outlier: 3.712A pdb=" N CYS O 115 " --> pdb=" O VAL O 111 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS O 116 " --> pdb=" O ASP O 112 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG O 117 " --> pdb=" O MET O 113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE O 118 " --> pdb=" O LEU O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 181 removed outlier: 3.507A pdb=" N SER O 177 " --> pdb=" O THR O 173 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS O 181 " --> pdb=" O SER O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 184 No H-bonds generated for 'chain 'O' and resid 182 through 184' Processing helix chain 'O' and resid 185 through 189 Processing helix chain 'O' and resid 193 through 207 removed outlier: 3.740A pdb=" N THR O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL O 205 " --> pdb=" O CYS O 201 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU O 206 " --> pdb=" O LEU O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 241 removed outlier: 3.579A pdb=" N ALA O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS O 238 " --> pdb=" O GLU O 234 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA O 241 " --> pdb=" O ALA O 237 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 30 removed outlier: 3.798A pdb=" N ALA P 26 " --> pdb=" O GLU P 22 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA P 27 " --> pdb=" O TYR P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 101 removed outlier: 3.532A pdb=" N ARG P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL P 84 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU P 85 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 120 removed outlier: 3.526A pdb=" N ARG P 112 " --> pdb=" O GLN P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 177 removed outlier: 3.517A pdb=" N THR P 171 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE P 172 " --> pdb=" O ASN P 168 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU P 174 " --> pdb=" O LYS P 170 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS P 175 " --> pdb=" O THR P 171 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG P 176 " --> pdb=" O PHE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 197 removed outlier: 4.046A pdb=" N HIS P 188 " --> pdb=" O GLU P 184 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR P 189 " --> pdb=" O ASP P 185 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU P 194 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER P 197 " --> pdb=" O THR P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 207 removed outlier: 3.961A pdb=" N ILE P 207 " --> pdb=" O GLU P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 230 removed outlier: 3.592A pdb=" N ASP P 227 " --> pdb=" O THR P 223 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR P 228 " --> pdb=" O GLU P 224 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA P 230 " --> pdb=" O LYS P 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 30 removed outlier: 3.648A pdb=" N GLU Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 102 removed outlier: 3.879A pdb=" N ASN Q 84 " --> pdb=" O THR Q 80 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL Q 85 " --> pdb=" O SER Q 81 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 124 removed outlier: 3.551A pdb=" N VAL Q 111 " --> pdb=" O CYS Q 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 176 Processing helix chain 'Q' and resid 185 through 200 removed outlier: 4.055A pdb=" N LYS Q 199 " --> pdb=" O LYS Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 247 removed outlier: 3.698A pdb=" N LEU Q 236 " --> pdb=" O GLU Q 232 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA Q 245 " --> pdb=" O GLU Q 241 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS Q 246 " --> pdb=" O GLU Q 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 27 removed outlier: 3.633A pdb=" N VAL R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.674A pdb=" N ILE R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 121 removed outlier: 3.799A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 176 removed outlier: 3.663A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 199 removed outlier: 3.738A pdb=" N VAL R 191 " --> pdb=" O THR R 187 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 232 removed outlier: 3.763A pdb=" N LYS R 227 " --> pdb=" O GLU R 223 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR R 228 " --> pdb=" O GLU R 224 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.575A pdb=" N GLU S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS S 32 " --> pdb=" O ILE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 85 through 104 Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 173 through 185 removed outlier: 6.818A pdb=" N SER S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER S 180 " --> pdb=" O GLY S 176 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU S 183 " --> pdb=" O SER S 179 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL S 184 " --> pdb=" O SER S 180 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 206 removed outlier: 3.531A pdb=" N LEU S 199 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE S 201 " --> pdb=" O SER S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 230 through 241 removed outlier: 3.725A pdb=" N GLU S 235 " --> pdb=" O LYS S 231 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU S 236 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL S 237 " --> pdb=" O GLU S 233 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP S 240 " --> pdb=" O GLU S 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 29 removed outlier: 3.504A pdb=" N GLU T 23 " --> pdb=" O ILE T 19 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 99 removed outlier: 3.700A pdb=" N PHE T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 122 removed outlier: 3.817A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Proline residue: T 119 - end of helix removed outlier: 3.503A pdb=" N ARG T 122 " --> pdb=" O ILE T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 176 Processing helix chain 'T' and resid 178 through 182 Processing helix chain 'T' and resid 183 through 197 removed outlier: 3.702A pdb=" N VAL T 188 " --> pdb=" O LEU T 184 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS T 189 " --> pdb=" O ASN T 185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS T 190 " --> pdb=" O GLU T 186 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY T 191 " --> pdb=" O LEU T 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU T 197 " --> pdb=" O ARG T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 234 Processing helix chain 'U' and resid 6 through 10 removed outlier: 4.306A pdb=" N SER U 10 " --> pdb=" O TYR U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 32 removed outlier: 3.530A pdb=" N LYS U 28 " --> pdb=" O GLU U 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA U 29 " --> pdb=" O TYR U 25 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU U 31 " --> pdb=" O MET U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 103 removed outlier: 3.641A pdb=" N SER U 86 " --> pdb=" O ALA U 82 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE U 98 " --> pdb=" O GLU U 94 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 121 removed outlier: 3.573A pdb=" N ASP U 113 " --> pdb=" O LYS U 109 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 178 removed outlier: 4.174A pdb=" N ALA U 172 " --> pdb=" O ALA U 168 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS U 173 " --> pdb=" O ARG U 169 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU U 175 " --> pdb=" O ALA U 171 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS U 178 " --> pdb=" O THR U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 201 removed outlier: 3.992A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU U 192 " --> pdb=" O ASP U 188 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS U 195 " --> pdb=" O LYS U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 244 removed outlier: 3.567A pdb=" N SER U 242 " --> pdb=" O TYR U 238 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS U 244 " --> pdb=" O LYS U 240 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 71 removed outlier: 3.565A pdb=" N ALA V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU V 69 " --> pdb=" O PHE V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.573A pdb=" N ALA V 79 " --> pdb=" O LEU V 75 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU V 82 " --> pdb=" O THR V 78 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG V 89 " --> pdb=" O GLU V 85 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 134 removed outlier: 3.528A pdb=" N TYR V 134 " --> pdb=" O GLY V 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 142 removed outlier: 3.519A pdb=" N ALA V 141 " --> pdb=" O GLY V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 167 removed outlier: 3.510A pdb=" N GLN V 154 " --> pdb=" O GLU V 150 " (cutoff:3.500A) Processing helix chain 'V' and resid 190 through 194 removed outlier: 3.878A pdb=" N ILE V 194 " --> pdb=" O GLY V 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 71 removed outlier: 3.697A pdb=" N LEU W 58 " --> pdb=" O MET W 54 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER W 69 " --> pdb=" O LEU W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 90 Processing helix chain 'W' and resid 130 through 142 removed outlier: 4.042A pdb=" N ALA W 136 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE W 138 " --> pdb=" O ALA W 134 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 164 removed outlier: 3.531A pdb=" N GLY W 162 " --> pdb=" O ALA W 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 1 through 5 Processing helix chain 'X' and resid 55 through 78 Processing helix chain 'X' and resid 82 through 97 removed outlier: 3.846A pdb=" N SER X 88 " --> pdb=" O TYR X 84 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS X 97 " --> pdb=" O LEU X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 153 removed outlier: 3.590A pdb=" N TYR X 146 " --> pdb=" O ALA X 142 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY X 147 " --> pdb=" O GLU X 143 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET X 148 " --> pdb=" O GLN X 144 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU X 150 " --> pdb=" O TYR X 146 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER X 151 " --> pdb=" O GLY X 147 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU X 152 " --> pdb=" O MET X 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 175 removed outlier: 3.555A pdb=" N GLU X 164 " --> pdb=" O ASP X 160 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN X 172 " --> pdb=" O GLN X 168 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA X 173 " --> pdb=" O ALA X 169 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 72 removed outlier: 3.743A pdb=" N GLN Y 55 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU Y 58 " --> pdb=" O VAL Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 90 removed outlier: 3.851A pdb=" N ASN Y 87 " --> pdb=" O PHE Y 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU Y 88 " --> pdb=" O THR Y 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 143 removed outlier: 4.628A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 170 removed outlier: 3.538A pdb=" N GLU Y 166 " --> pdb=" O LYS Y 162 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU Y 167 " --> pdb=" O CYS Y 163 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN Y 168 " --> pdb=" O LEU Y 164 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS Y 169 " --> pdb=" O GLU Y 165 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 71 removed outlier: 3.600A pdb=" N GLU Z 56 " --> pdb=" O CYS Z 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 88 removed outlier: 3.508A pdb=" N VAL Z 87 " --> pdb=" O LEU Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 4.250A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG Z 141 " --> pdb=" O GLY Z 137 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY Z 142 " --> pdb=" O VAL Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 removed outlier: 3.623A pdb=" N ASP Z 154 " --> pdb=" O GLU Z 150 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU Z 155 " --> pdb=" O GLN Z 151 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE Z 160 " --> pdb=" O ALA Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 191 through 199 removed outlier: 4.218A pdb=" N GLU Z 197 " --> pdb=" O ALA Z 193 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS Z 198 " --> pdb=" O ASP Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 80 removed outlier: 3.788A pdb=" N LYS a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET a 74 " --> pdb=" O ALA a 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR a 75 " --> pdb=" O ARG a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 99 removed outlier: 3.553A pdb=" N THR a 94 " --> pdb=" O ALA a 90 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 153 Proline residue: a 147 - end of helix Processing helix chain 'a' and resid 167 through 186 removed outlier: 3.521A pdb=" N MET a 172 " --> pdb=" O LEU a 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE a 179 " --> pdb=" O VAL a 175 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE a 180 " --> pdb=" O LYS a 176 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER a 181 " --> pdb=" O ASP a 177 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG a 185 " --> pdb=" O SER a 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 78 removed outlier: 3.538A pdb=" N GLN b 69 " --> pdb=" O GLN b 65 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET b 70 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE b 72 " --> pdb=" O GLY b 68 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU b 77 " --> pdb=" O ASP b 73 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 102 removed outlier: 3.503A pdb=" N ARG b 99 " --> pdb=" O ALA b 95 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG b 100 " --> pdb=" O MET b 96 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS b 102 " --> pdb=" O SER b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 146 Processing helix chain 'b' and resid 146 through 157 removed outlier: 3.925A pdb=" N LYS b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 180 removed outlier: 3.570A pdb=" N ARG b 179 " --> pdb=" O VAL b 175 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 5.784A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 52 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 216 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 217 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 removed outlier: 4.590A pdb=" N VAL A 151 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.563A pdb=" N GLY B 36 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.559A pdb=" N GLU B 65 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 132 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.556A pdb=" N ILE C 37 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 44 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.739A pdb=" N SER C 75 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 138 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY C 158 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.580A pdb=" N HIS D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.656A pdb=" N VAL D 41 " --> pdb=" O MET D 211 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL D 210 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS D 218 " --> pdb=" O VAL D 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AB1, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 69 removed outlier: 4.333A pdb=" N LEU E 153 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN E 164 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.933A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 70 through 76 Processing sheet with id=AB5, first strand: chain 'F' and resid 70 through 76 Processing sheet with id=AB6, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.606A pdb=" N TRP G 215 " --> pdb=" O GLU G 225 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU G 225 " --> pdb=" O TRP G 215 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY G 217 " --> pdb=" O ARG G 223 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG G 223 " --> pdb=" O GLY G 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 66 through 68 removed outlier: 3.528A pdb=" N PHE G 135 " --> pdb=" O ILE G 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 125 through 128 removed outlier: 3.663A pdb=" N GLY H 11 " --> pdb=" O PHE H 8 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA H 177 " --> pdb=" O LEU H 14 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.189A pdb=" N THR H 22 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE H 26 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 41 through 47 removed outlier: 3.586A pdb=" N ALA H 101 " --> pdb=" O PHE H 42 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE H 99 " --> pdb=" O CYS H 44 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL H 121 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 124 through 127 removed outlier: 3.744A pdb=" N VAL I 125 " --> pdb=" O GLY I 5 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE I 173 " --> pdb=" O PRO I 188 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU I 175 " --> pdb=" O LEU I 186 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.021A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 35 through 36 removed outlier: 3.532A pdb=" N CYS I 43 " --> pdb=" O HIS I 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 213 through 218 removed outlier: 3.522A pdb=" N THR I 213 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA J 9 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 41 through 45 removed outlier: 3.666A pdb=" N ILE J 50 " --> pdb=" O PHE J 42 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU J 48 " --> pdb=" O MET J 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 129 through 132 removed outlier: 3.615A pdb=" N LEU K 4 " --> pdb=" O HIS K 132 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL K 15 " --> pdb=" O ARG K 181 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG K 181 " --> pdb=" O VAL K 15 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 35 through 37 removed outlier: 3.660A pdb=" N LEU K 104 " --> pdb=" O TYR K 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.547A pdb=" N ALA L 5 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL L 12 " --> pdb=" O VAL L 179 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU L 176 " --> pdb=" O VAL L 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 22 removed outlier: 7.405A pdb=" N ALA L 20 " --> pdb=" O ALA L 27 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 34 through 38 removed outlier: 3.566A pdb=" N ILE L 37 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR L 44 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY L 103 " --> pdb=" O GLY L 110 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.793A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 29 through 31 removed outlier: 7.052A pdb=" N LEU M 29 " --> pdb=" O HIS M 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 43 through 45 removed outlier: 3.583A pdb=" N ILE M 109 " --> pdb=" O GLY M 53 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN M 108 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 7 through 8 removed outlier: 3.506A pdb=" N GLY N 55 " --> pdb=" O GLY N 8 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 7 through 8 removed outlier: 3.506A pdb=" N GLY N 55 " --> pdb=" O GLY N 8 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR N 132 " --> pdb=" O TYR N 124 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 14 through 16 removed outlier: 3.640A pdb=" N GLY N 19 " --> pdb=" O PHE N 16 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.783A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR O 52 " --> pdb=" O GLU O 216 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU O 216 " --> pdb=" O THR O 52 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL O 217 " --> pdb=" O LEU O 230 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 69 through 71 removed outlier: 4.589A pdb=" N VAL O 151 " --> pdb=" O PHE O 163 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 159 through 162 removed outlier: 3.563A pdb=" N GLY P 36 " --> pdb=" O THR P 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 65 through 68 removed outlier: 3.560A pdb=" N GLU P 65 " --> pdb=" O LEU P 73 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE P 71 " --> pdb=" O ILE P 67 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER P 132 " --> pdb=" O SER P 76 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 161 through 164 removed outlier: 3.556A pdb=" N ILE Q 37 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU Q 44 " --> pdb=" O ILE Q 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 72 through 75 removed outlier: 3.739A pdb=" N SER Q 75 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY Q 138 " --> pdb=" O GLN Q 146 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU Q 147 " --> pdb=" O TRP Q 159 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY Q 158 " --> pdb=" O ASP R 55 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 10 through 11 removed outlier: 3.579A pdb=" N HIS R 15 " --> pdb=" O SER R 11 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 158 through 161 removed outlier: 3.655A pdb=" N VAL R 41 " --> pdb=" O MET R 211 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL R 210 " --> pdb=" O LYS R 218 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS R 218 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 62 through 64 Processing sheet with id=AE9, first strand: chain 'S' and resid 167 through 170 Processing sheet with id=AF1, first strand: chain 'S' and resid 67 through 69 removed outlier: 4.333A pdb=" N LEU S 153 " --> pdb=" O CYS S 165 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN S 164 " --> pdb=" O ALA T 58 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 158 through 161 removed outlier: 3.932A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 70 through 76 Processing sheet with id=AF4, first strand: chain 'T' and resid 70 through 76 Processing sheet with id=AF5, first strand: chain 'U' and resid 162 through 165 removed outlier: 3.605A pdb=" N TRP U 215 " --> pdb=" O GLU U 225 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU U 225 " --> pdb=" O TRP U 215 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY U 217 " --> pdb=" O ARG U 223 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG U 223 " --> pdb=" O GLY U 217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 66 through 68 removed outlier: 3.528A pdb=" N PHE U 135 " --> pdb=" O ILE U 151 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 125 through 128 removed outlier: 3.663A pdb=" N GLY V 11 " --> pdb=" O PHE V 8 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA V 177 " --> pdb=" O LEU V 14 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.189A pdb=" N THR V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE V 26 " --> pdb=" O THR V 22 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 41 through 47 removed outlier: 3.586A pdb=" N ALA V 101 " --> pdb=" O PHE V 42 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE V 99 " --> pdb=" O CYS V 44 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL V 121 " --> pdb=" O SER V 113 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 124 through 127 removed outlier: 3.744A pdb=" N VAL W 125 " --> pdb=" O GLY W 5 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE W 173 " --> pdb=" O PRO W 188 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU W 175 " --> pdb=" O LEU W 186 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.022A pdb=" N GLU W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL W 26 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 35 through 36 removed outlier: 3.531A pdb=" N CYS W 43 " --> pdb=" O HIS W 35 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 213 through 218 removed outlier: 3.521A pdb=" N THR W 213 " --> pdb=" O THR X 198 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA X 9 " --> pdb=" O ASP X 24 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 41 through 45 removed outlier: 3.666A pdb=" N ILE X 50 " --> pdb=" O PHE X 42 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU X 48 " --> pdb=" O MET X 44 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 129 through 132 removed outlier: 3.617A pdb=" N LEU Y 4 " --> pdb=" O HIS Y 132 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL Y 15 " --> pdb=" O ARG Y 181 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG Y 181 " --> pdb=" O VAL Y 15 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 35 through 37 removed outlier: 3.659A pdb=" N LEU Y 104 " --> pdb=" O TYR Y 116 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 125 through 129 removed outlier: 3.547A pdb=" N ALA Z 5 " --> pdb=" O PHE Z 126 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL Z 12 " --> pdb=" O VAL Z 179 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU Z 176 " --> pdb=" O VAL Z 187 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 20 through 22 removed outlier: 7.405A pdb=" N ALA Z 20 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.567A pdb=" N ILE Z 37 " --> pdb=" O LEU Z 41 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR Z 44 " --> pdb=" O MET Z 100 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY Z 103 " --> pdb=" O GLY Z 110 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'a' and resid 135 through 139 removed outlier: 5.794A pdb=" N THR a 11 " --> pdb=" O ASP a 26 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 29 through 31 removed outlier: 7.052A pdb=" N LEU a 29 " --> pdb=" O HIS a 36 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 43 through 45 removed outlier: 3.583A pdb=" N ILE a 109 " --> pdb=" O GLY a 53 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN a 108 " --> pdb=" O PHE a 124 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL a 121 " --> pdb=" O ASP a 133 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 7 through 8 removed outlier: 3.506A pdb=" N GLY b 55 " --> pdb=" O GLY b 8 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 7 through 8 removed outlier: 3.506A pdb=" N GLY b 55 " --> pdb=" O GLY b 8 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR b 132 " --> pdb=" O TYR b 124 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 14 through 16 removed outlier: 3.641A pdb=" N GLY b 19 " --> pdb=" O PHE b 16 " (cutoff:3.500A) 2343 hydrogen bonds defined for protein. 6630 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: 17.50 Time building geometry restraints manager: 17.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14838 1.34 - 1.46: 9965 1.46 - 1.58: 20917 1.58 - 1.69: 0 1.69 - 1.81: 462 Bond restraints: 46182 Sorted by residual: bond pdb=" C ARG W 187 " pdb=" O ARG W 187 " ideal model delta sigma weight residual 1.244 1.230 0.013 9.10e-03 1.21e+04 2.17e+00 bond pdb=" C ARG I 187 " pdb=" O ARG I 187 " ideal model delta sigma weight residual 1.244 1.231 0.013 9.10e-03 1.21e+04 1.94e+00 bond pdb=" C ASN L 38 " pdb=" N PRO L 39 " ideal model delta sigma weight residual 1.334 1.352 -0.018 1.51e-02 4.39e+03 1.38e+00 bond pdb=" CA PHE A 187 " pdb=" C PHE A 187 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.50e-02 4.44e+03 1.26e+00 bond pdb=" N ARG D 213 " pdb=" CA ARG D 213 " ideal model delta sigma weight residual 1.468 1.454 0.014 1.24e-02 6.50e+03 1.25e+00 ... (remaining 46177 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.41: 1079 106.41 - 113.31: 25119 113.31 - 120.22: 16472 120.22 - 127.13: 19691 127.13 - 134.03: 347 Bond angle restraints: 62708 Sorted by residual: angle pdb=" CA ARG W 187 " pdb=" C ARG W 187 " pdb=" N PRO W 188 " ideal model delta sigma weight residual 120.58 116.55 4.03 7.40e-01 1.83e+00 2.96e+01 angle pdb=" CA ARG I 187 " pdb=" C ARG I 187 " pdb=" N PRO I 188 " ideal model delta sigma weight residual 120.58 116.64 3.94 7.40e-01 1.83e+00 2.84e+01 angle pdb=" C GLN X 30 " pdb=" N ALA X 31 " pdb=" CA ALA X 31 " ideal model delta sigma weight residual 122.95 117.29 5.66 1.44e+00 4.82e-01 1.54e+01 angle pdb=" C GLN J 30 " pdb=" N ALA J 31 " pdb=" CA ALA J 31 " ideal model delta sigma weight residual 122.95 117.35 5.60 1.44e+00 4.82e-01 1.51e+01 angle pdb=" O ARG W 187 " pdb=" C ARG W 187 " pdb=" N PRO W 188 " ideal model delta sigma weight residual 120.27 122.87 -2.60 6.90e-01 2.10e+00 1.42e+01 ... (remaining 62703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 26860 16.05 - 32.09: 404 32.09 - 48.14: 118 48.14 - 64.19: 12 64.19 - 80.23: 22 Dihedral angle restraints: 27416 sinusoidal: 9534 harmonic: 17882 Sorted by residual: dihedral pdb=" CA GLN F 60 " pdb=" C GLN F 60 " pdb=" N LYS F 61 " pdb=" CA LYS F 61 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLN T 60 " pdb=" C GLN T 60 " pdb=" N LYS T 61 " pdb=" CA LYS T 61 " ideal model delta harmonic sigma weight residual 180.00 151.78 28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA PHE C 60 " pdb=" C PHE C 60 " pdb=" N PHE C 61 " pdb=" CA PHE C 61 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 27413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 6602 0.070 - 0.139: 727 0.139 - 0.209: 14 0.209 - 0.279: 2 0.279 - 0.348: 1 Chirality restraints: 7346 Sorted by residual: chirality pdb=" CA PHE A 187 " pdb=" N PHE A 187 " pdb=" C PHE A 187 " pdb=" CB PHE A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA SER R 216 " pdb=" N SER R 216 " pdb=" C SER R 216 " pdb=" CB SER R 216 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA SER D 216 " pdb=" N SER D 216 " pdb=" C SER D 216 " pdb=" CB SER D 216 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 7343 not shown) Planarity restraints: 7974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL O 183 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C VAL O 183 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL O 183 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS O 184 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER I 38 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO I 39 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO I 39 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 39 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER W 38 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO W 39 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO W 39 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO W 39 " -0.027 5.00e-02 4.00e+02 ... (remaining 7971 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1211 2.70 - 3.25: 43944 3.25 - 3.80: 71841 3.80 - 4.35: 94907 4.35 - 4.90: 160145 Nonbonded interactions: 372048 Sorted by model distance: nonbonded pdb=" O LYS M 49 " pdb=" OG1 THR M 50 " model vdw 2.155 2.440 nonbonded pdb=" O LYS a 49 " pdb=" OG1 THR a 50 " model vdw 2.156 2.440 nonbonded pdb=" O GLY D 140 " pdb=" NH2 ARG D 213 " model vdw 2.215 2.520 nonbonded pdb=" O GLY R 140 " pdb=" NH2 ARG R 213 " model vdw 2.222 2.520 nonbonded pdb=" O GLN R 116 " pdb=" OG1 THR R 119 " model vdw 2.227 2.440 ... (remaining 372043 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 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 0.040 Extract box with map and model: 4.780 Check model and map are aligned: 0.690 Set scattering table: 0.460 Process input model: 113.540 Find NCS groups from input model: 4.420 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 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 : 0.002 0.018 46182 Z= 0.133 Angle : 0.613 7.999 62708 Z= 0.400 Chirality : 0.043 0.348 7346 Planarity : 0.004 0.049 7974 Dihedral : 7.670 80.232 16000 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -2.87 (0.09), residues: 6142 helix: -3.32 (0.07), residues: 2082 sheet: -0.95 (0.12), residues: 1468 loop : -0.96 (0.10), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 215 HIS 0.007 0.001 HIS B 87 PHE 0.020 0.001 PHE F 145 TYR 0.018 0.001 TYR X 146 ARG 0.003 0.000 ARG R 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1951 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1951 time to evaluate : 4.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.6607 (m-10) cc_final: 0.6229 (m-10) REVERT: A 175 SER cc_start: 0.8243 (p) cc_final: 0.7854 (p) REVERT: A 235 ILE cc_start: 0.8467 (mt) cc_final: 0.8095 (tt) REVERT: B 71 ILE cc_start: 0.8561 (mt) cc_final: 0.8343 (mt) REVERT: B 99 VAL cc_start: 0.7852 (t) cc_final: 0.7184 (t) REVERT: B 160 THR cc_start: 0.7034 (t) cc_final: 0.6796 (m) REVERT: D 21 TYR cc_start: 0.7675 (m-10) cc_final: 0.7340 (m-80) REVERT: D 68 ASN cc_start: 0.7508 (p0) cc_final: 0.7146 (p0) REVERT: D 110 TYR cc_start: 0.6159 (t80) cc_final: 0.5767 (t80) REVERT: E 76 CYS cc_start: 0.7089 (t) cc_final: 0.6337 (t) REVERT: E 101 PHE cc_start: 0.7252 (t80) cc_final: 0.6929 (t80) REVERT: E 107 MET cc_start: 0.7396 (ttt) cc_final: 0.7162 (ttt) REVERT: E 137 PHE cc_start: 0.8166 (m-80) cc_final: 0.7577 (m-10) REVERT: E 143 PHE cc_start: 0.7279 (m-80) cc_final: 0.6866 (m-80) REVERT: G 110 HIS cc_start: 0.7056 (t-170) cc_final: 0.6780 (t70) REVERT: I 209 THR cc_start: 0.6525 (m) cc_final: 0.6186 (t) REVERT: J 196 THR cc_start: 0.8479 (m) cc_final: 0.8213 (p) REVERT: O 78 CYS cc_start: 0.8039 (t) cc_final: 0.7561 (t) REVERT: O 163 PHE cc_start: 0.4977 (m-80) cc_final: 0.4685 (m-80) REVERT: P 228 TYR cc_start: 0.5873 (m-80) cc_final: 0.5450 (m-80) REVERT: Q 30 HIS cc_start: 0.6255 (m-70) cc_final: 0.6017 (m-70) REVERT: R 10 PHE cc_start: 0.4951 (m-80) cc_final: 0.4727 (m-80) REVERT: V 65 PHE cc_start: 0.7426 (t80) cc_final: 0.6829 (t80) REVERT: V 104 ASP cc_start: 0.4741 (p0) cc_final: 0.4246 (p0) REVERT: X 192 ASP cc_start: 0.6235 (p0) cc_final: 0.6006 (p0) REVERT: Y 11 ASP cc_start: 0.5266 (p0) cc_final: 0.48------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 127 GLN A 193 GLN B 94 GLN C 40 ASN C 167 ASN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 92 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 178 GLN F 43 HIS ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN F 175 HIS G 180 GLN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 HIS ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS M 8 ASN M 108 ASN N 38 ASN N 81 HIS O 24 GLN O 75 ASN O 90 GLN O 128 ASN ** O 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN Q 40 ASN Q 109 GLN R 54 GLN R 146 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 152 GLN S 164 GLN T 43 HIS T 65 HIS T 90 GLN T 121 GLN U 101 ASN ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 66 HIS X 64 GLN ** X 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 175 ASN a 8 ASN a 79 ASN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 131 GLN a 157 ASN ** a 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 61 GLN b 108 ASN b 147 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 46182 Z= 0.234 Angle : 0.681 10.038 62708 Z= 0.356 Chirality : 0.046 0.191 7346 Planarity : 0.005 0.074 7974 Dihedral : 4.573 28.086 6788 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.94 % Favored : 98.03 % Rotamer: Outliers : 3.77 % Allowed : 15.53 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.10), residues: 6142 helix: -0.79 (0.10), residues: 2168 sheet: -0.42 (0.12), residues: 1444 loop : -0.64 (0.11), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 104 HIS 0.008 0.001 HIS S 99 PHE 0.026 0.002 PHE S 143 TYR 0.029 0.002 TYR Q 136 ARG 0.011 0.001 ARG O 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1178 time to evaluate : 4.120 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: A 235 ILE cc_start: 0.8655 (mt) cc_final: 0.8296 (tt) REVERT: B 112 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7592 (mmt90) REVERT: C 98 LEU cc_start: 0.8266 (mp) cc_final: 0.7921 (tt) REVERT: D 21 TYR cc_start: 0.7910 (m-10) cc_final: 0.7632 (m-80) REVERT: D 228 TYR cc_start: 0.7102 (m-80) cc_final: 0.6797 (m-10) REVERT: E 152 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7694 (mp-120) REVERT: G 111 LEU cc_start: 0.9094 (tt) cc_final: 0.8830 (tt) REVERT: H 65 PHE cc_start: 0.7862 (t80) cc_final: 0.6899 (t80) REVERT: H 87 CYS cc_start: 0.7523 (p) cc_final: 0.7221 (t) REVERT: I 24 MET cc_start: 0.7652 (ppp) cc_final: 0.6910 (ppp) REVERT: J 3 MET cc_start: 0.7336 (mmm) cc_final: 0.6710 (mmm) REVERT: J 49 TYR cc_start: 0.8031 (m-80) cc_final: 0.7707 (m-80) REVERT: K 13 VAL cc_start: 0.7644 (OUTLIER) cc_final: 0.7322 (t) REVERT: K 160 LEU cc_start: 0.8803 (tt) cc_final: 0.8427 (tt) REVERT: K 177 THR cc_start: 0.7886 (p) cc_final: 0.7442 (p) REVERT: L 86 MET cc_start: 0.6738 (mtm) cc_final: 0.6311 (mtp) REVERT: M 83 MET cc_start: 0.8487 (tpp) cc_final: 0.8118 (tpp) REVERT: N 26 MET cc_start: 0.7070 (pmm) cc_final: 0.6672 (pmm) REVERT: N 76 LEU cc_start: 0.7886 (mt) cc_final: 0.7591 (mt) REVERT: O 78 CYS cc_start: 0.7192 (t) cc_final: 0.6724 (t) REVERT: P 102 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6769 (tm-30) REVERT: Q 88 ASN cc_start: 0.7725 (t0) cc_final: 0.7283 (t0) REVERT: Q 100 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7565 (tp40) REVERT: Q 124 PHE cc_start: 0.7454 (p90) cc_final: 0.7091 (p90) REVERT: R 71 MET cc_start: 0.7675 (ppp) cc_final: 0.7108 (ptm) REVERT: R 84 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8235 (mt) REVERT: U 51 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7564 (ptpt) REVERT: V 65 PHE cc_start: 0.7376 (t80) cc_final: 0.6907 (t80) REVERT: V 133 SER cc_start: 0.7381 (p) cc_final: 0.6880 (t) REVERT: W 37 ILE cc_start: 0.5520 (OUTLIER) cc_final: 0.5301 (mt) REVERT: X 3 MET cc_start: 0.7033 (mmm) cc_final: 0.6653 (mmm) REVERT: X 157 MET cc_start: 0.6180 (tpp) cc_final: 0.5874 (mmm) REVERT: X 175 ASP cc_start: 0.6807 (p0) cc_final: 0.6570 (p0) REVERT: X 192 ASP cc_start: 0.6304 (p0) cc_final: 0.6025 (p0) REVERT: Y 11 ASP cc_start: 0.5200 (p0) cc_final: 0.4950 (p0) REVERT: Y 87 ASN cc_start: 0.6982 (p0) cc_final: 0.6514 (p0) REVERT: a 83 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7493 (mpp) REVERT: a 205 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6927 (tt0) REVERT: b 50 MET cc_start: 0.7526 (tmm) cc_final: 0.7281 (tmm) REVERT: b 56 ASP cc_start: 0.7193 (t0) cc_final: 0.6757 (t0) REVERT: b 76 LEU cc_start: 0.7504 (mt) cc_final: 0.6973 (mt) REVERT: b 127 MET cc_start: 0.6882 (ptp) cc_final: 0.6625 (ptm) REVERT: b 173 MET cc_start: 0.7078 (tpp) cc_final: 0.6808 (mmt) outliers start: 161 outliers final: 85 residues processed: 1266 average time/residue: 0.5360 time to fit residues: 1110.0410 Evaluate side-chains 1052 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 960 time to evaluate : 4.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 134 TYR Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 193 GLN Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 166 TYR Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 213 ILE Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain T residue 68 ASN Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 51 LYS Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain U residue 206 ASP Chi-restraints excluded: chain V residue 91 ARG Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain W residue 10 ASP Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain X residue 105 GLU Chi-restraints excluded: chain X residue 146 TYR Chi-restraints excluded: chain X residue 163 PHE Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain a residue 205 GLU Chi-restraints excluded: chain b residue 98 SER Chi-restraints excluded: chain b residue 108 ASN Chi-restraints excluded: chain b residue 147 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 307 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 461 optimal weight: 20.0000 chunk 377 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 554 optimal weight: 9.9990 chunk 599 optimal weight: 5.9990 chunk 494 optimal weight: 10.0000 chunk 550 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 445 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: