Starting phenix.real_space_refine on Wed Apr 17 16:55:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pg9_13389/04_2024/7pg9_13389.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pg9_13389/04_2024/7pg9_13389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pg9_13389/04_2024/7pg9_13389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pg9_13389/04_2024/7pg9_13389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pg9_13389/04_2024/7pg9_13389.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pg9_13389/04_2024/7pg9_13389.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 28984 2.51 5 N 8007 2.21 5 O 8055 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 TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "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 8": "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 "J PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 12": "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 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 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 TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 166": "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 8": "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 "X PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 12": "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 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 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 99": "NH1" <-> "NH2" Residue "a ARG 173": "NH1" <-> "NH2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "b TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 45326 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1729 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 85 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: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1725 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 8, 'TRANS': 229} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 85 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: 23.69, per 1000 atoms: 0.52 Number of scatterers: 45326 At special positions: 0 Unit cell: (192.428, 158.16, 133.118, 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 8055 8.00 N 8007 7.00 C 28984 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: 16.35 Conformation dependent library (CDL) restraints added in 8.9 seconds 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11412 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 70 sheets defined 39.1% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 removed outlier: 3.852A pdb=" N ASP A 10 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG A 11 " --> pdb=" O GLY A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.899A pdb=" N PHE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.501A pdb=" N GLY A 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 106 removed outlier: 3.756A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.635A pdb=" N CYS A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.604A 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 Processing helix chain 'A' and resid 193 through 207 removed outlier: 3.721A pdb=" N THR A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.518A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 30 removed outlier: 3.651A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 101 removed outlier: 3.546A pdb=" N ARG B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 123 removed outlier: 3.537A pdb=" N GLN B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.597A pdb=" N PHE B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.923A pdb=" N HIS B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 removed outlier: 3.535A pdb=" N LYS B 226 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.704A pdb=" N GLU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.685A pdb=" N ASN C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 removed outlier: 3.503A pdb=" N THR C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 4.172A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 200 removed outlier: 4.047A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 247 removed outlier: 3.718A pdb=" N ALA C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 Processing helix chain 'D' and resid 76 through 99 removed outlier: 3.603A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.535A pdb=" N TYR D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.672A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 removed outlier: 3.523A pdb=" N ILE D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 232 removed outlier: 3.610A pdb=" N GLU D 226 " --> pdb=" O PRO D 222 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.722A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.658A 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 81 through 104 removed outlier: 3.871A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 173 through 185 removed outlier: 6.653A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 removed outlier: 3.556A pdb=" N LEU E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.600A pdb=" N GLU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 29 removed outlier: 3.740A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 99 removed outlier: 3.748A pdb=" N PHE F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.527A pdb=" N SER F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix removed outlier: 3.547A pdb=" N ARG F 122 " --> pdb=" O ILE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 176 removed outlier: 4.096A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.577A pdb=" N VAL F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'G' and resid 6 through 10 removed outlier: 3.704A pdb=" N LEU G 9 " --> pdb=" O GLY G 6 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER G 10 " --> pdb=" O TYR G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 10' Processing helix chain 'G' and resid 20 through 27 Processing helix chain 'G' and resid 27 through 32 removed outlier: 3.528A pdb=" N GLU G 31 " --> pdb=" O MET G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 103 Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.552A pdb=" N ASP G 113 " --> pdb=" O LYS G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 removed outlier: 4.210A pdb=" N ALA G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS G 173 " --> pdb=" O ARG G 169 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS G 178 " --> pdb=" O THR G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 4.025A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 244 Processing helix chain 'H' and resid 48 through 71 removed outlier: 3.871A pdb=" N GLU H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.936A pdb=" N ARG H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 134 removed outlier: 3.700A pdb=" N SER H 133 " --> pdb=" O SER H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 142 Processing helix chain 'H' and resid 148 through 167 removed outlier: 3.676A pdb=" N GLN H 154 " --> pdb=" O GLU H 150 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.791A pdb=" N ILE H 194 " --> pdb=" O GLY H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 71 removed outlier: 3.761A pdb=" N LEU I 58 " --> pdb=" O MET I 54 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 90 Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.950A pdb=" N ALA I 136 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 164 removed outlier: 3.522A 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 removed outlier: 3.552A pdb=" N LEU J 72 " --> pdb=" O PHE J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 97 removed outlier: 3.649A pdb=" N SER J 88 " --> pdb=" O TYR J 84 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 removed outlier: 4.262A pdb=" N GLY J 147 " --> pdb=" O GLU J 143 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET J 148 " --> pdb=" O GLN J 144 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU J 152 " --> pdb=" O MET J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 175 removed outlier: 3.505A pdb=" N GLU J 164 " --> pdb=" O ASP J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 72 removed outlier: 3.626A pdb=" N GLN K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU K 58 " --> pdb=" O VAL K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 90 removed outlier: 3.769A pdb=" N ASN K 87 " --> pdb=" O PHE K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 147 removed outlier: 4.651A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 170 removed outlier: 3.526A pdb=" N GLN K 168 " --> pdb=" O LEU K 164 " (cutoff:3.500A) removed outlier: 3.557A 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 GLN L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 89 removed outlier: 3.981A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 3.555A pdb=" N ALA L 135 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY L 142 " --> pdb=" O VAL L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 removed outlier: 3.642A pdb=" N ASP L 154 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE L 160 " --> pdb=" O ALA L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 199 removed outlier: 4.240A pdb=" N GLU L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 80 removed outlier: 3.832A pdb=" N LYS M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.539A pdb=" N SER M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) removed outlier: 3.744A 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: 3.512A pdb=" N MET M 172 " --> pdb=" O LEU M 168 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE M 180 " --> pdb=" O LYS M 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER M 181 " --> pdb=" O ASP M 177 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG M 185 " --> pdb=" O SER M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 78 removed outlier: 3.543A pdb=" N ILE N 72 " --> pdb=" O GLY N 68 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 removed outlier: 3.753A pdb=" N ARG N 100 " --> pdb=" O MET N 96 " (cutoff:3.500A) removed outlier: 3.730A 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: 3.829A pdb=" N LYS N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 180 Processing helix chain 'O' and resid 22 through 31 removed outlier: 3.543A pdb=" N TYR O 27 " --> pdb=" O TYR O 23 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE O 29 " --> pdb=" O VAL O 25 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 36 removed outlier: 3.501A pdb=" N GLY O 35 " --> pdb=" O ILE O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 106 removed outlier: 3.755A pdb=" N SER O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 128 removed outlier: 3.634A pdb=" N CYS O 115 " --> pdb=" O VAL O 111 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS O 116 " --> pdb=" O ASP O 112 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG O 117 " --> pdb=" O MET O 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE O 118 " --> pdb=" O LEU O 114 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL O 124 " --> pdb=" O ASP O 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR O 126 " --> pdb=" O SER O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 181 removed outlier: 3.604A 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: 3.721A pdb=" N THR O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL O 205 " --> pdb=" O CYS O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.518A pdb=" N ALA O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS O 238 " --> pdb=" O GLU O 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 30 removed outlier: 3.651A pdb=" N ALA P 26 " --> pdb=" O GLU P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 101 removed outlier: 3.547A pdb=" N ARG P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL P 84 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU P 85 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 123 removed outlier: 3.535A pdb=" N GLN P 111 " --> pdb=" O ALA P 107 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR P 120 " --> pdb=" O VAL P 116 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR P 121 " --> pdb=" O MET P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 177 removed outlier: 3.597A pdb=" N PHE P 172 " --> pdb=" O ASN P 168 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU P 174 " --> pdb=" O LYS P 170 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS P 175 " --> pdb=" O THR P 171 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG P 176 " --> pdb=" O PHE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 197 removed outlier: 3.924A pdb=" N HIS P 188 " --> pdb=" O GLU P 184 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR P 189 " --> pdb=" O ASP P 185 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER P 197 " --> pdb=" O THR P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 229 removed outlier: 3.535A pdb=" N LYS P 226 " --> pdb=" O PRO P 222 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR P 228 " --> pdb=" O GLU P 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 30 removed outlier: 3.705A pdb=" N GLU Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 102 removed outlier: 3.686A pdb=" N ASN Q 84 " --> pdb=" O THR Q 80 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL Q 85 " --> pdb=" O SER Q 81 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 124 removed outlier: 3.503A pdb=" N THR Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 179 removed outlier: 4.172A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR Q 179 " --> pdb=" O LEU Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 200 removed outlier: 4.047A pdb=" N LYS Q 199 " --> pdb=" O LYS Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 247 removed outlier: 3.718A pdb=" N ALA Q 245 " --> pdb=" O GLU Q 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 27 Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.604A pdb=" N ILE R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 121 removed outlier: 3.536A pdb=" N TYR R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 176 removed outlier: 3.672A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 199 removed outlier: 3.524A pdb=" N ILE R 188 " --> pdb=" O ASP R 184 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL R 191 " --> pdb=" O THR R 187 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 232 removed outlier: 3.610A pdb=" N GLU R 226 " --> pdb=" O PRO R 222 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS R 227 " --> pdb=" O GLU R 223 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR R 228 " --> pdb=" O GLU R 224 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.721A pdb=" N GLU S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 3.658A 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 81 through 104 removed outlier: 3.871A pdb=" N ALA S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS S 86 " --> pdb=" O ILE S 82 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 173 through 185 removed outlier: 6.653A pdb=" N SER S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER S 180 " --> pdb=" O GLY S 176 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU S 183 " --> pdb=" O SER S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 206 removed outlier: 3.556A pdb=" N LEU S 199 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE S 201 " --> pdb=" O SER S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 230 through 241 removed outlier: 3.600A pdb=" N GLU S 235 " --> pdb=" O LYS S 231 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU S 236 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL S 237 " --> pdb=" O GLU S 233 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP S 240 " --> pdb=" O GLU S 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 29 removed outlier: 3.739A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 99 removed outlier: 3.747A pdb=" N PHE T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 122 removed outlier: 3.528A pdb=" N SER T 110 " --> pdb=" O SER T 106 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Proline residue: T 119 - end of helix removed outlier: 3.547A pdb=" N ARG T 122 " --> pdb=" O ILE T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 176 removed outlier: 4.097A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 178 through 182 Processing helix chain 'T' and resid 183 through 197 removed outlier: 3.577A pdb=" N VAL T 188 " --> pdb=" O LEU T 184 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS T 189 " --> pdb=" O ASN T 185 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS T 190 " --> pdb=" O GLU T 186 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY T 191 " --> pdb=" O LEU T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 234 Processing helix chain 'U' and resid 6 through 10 removed outlier: 3.703A pdb=" N LEU U 9 " --> pdb=" O GLY U 6 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER U 10 " --> pdb=" O TYR U 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 6 through 10' Processing helix chain 'U' and resid 20 through 27 Processing helix chain 'U' and resid 27 through 32 removed outlier: 3.529A pdb=" N GLU U 31 " --> pdb=" O MET U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 103 Processing helix chain 'U' and resid 107 through 121 removed outlier: 3.553A pdb=" N ASP U 113 " --> pdb=" O LYS U 109 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 178 removed outlier: 4.209A pdb=" N ALA U 172 " --> pdb=" O ALA U 168 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS U 173 " --> pdb=" O ARG U 169 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU U 175 " --> pdb=" O ALA U 171 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS U 178 " --> pdb=" O THR U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 201 removed outlier: 4.024A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU U 192 " --> pdb=" O ASP U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 244 Processing helix chain 'V' and resid 48 through 71 removed outlier: 3.870A pdb=" N GLU V 69 " --> pdb=" O PHE V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.936A pdb=" N ARG V 89 " --> pdb=" O GLU V 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 134 removed outlier: 3.700A pdb=" N SER V 133 " --> pdb=" O SER V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 142 Processing helix chain 'V' and resid 148 through 167 removed outlier: 3.677A pdb=" N GLN V 154 " --> pdb=" O GLU V 150 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU V 165 " --> pdb=" O ALA V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 190 through 194 removed outlier: 3.791A pdb=" N ILE V 194 " --> pdb=" O GLY V 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 71 removed outlier: 3.761A pdb=" N LEU W 58 " --> pdb=" O MET W 54 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 90 Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.949A pdb=" N ALA W 136 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 164 removed outlier: 3.522A 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 removed outlier: 3.553A pdb=" N LEU X 72 " --> pdb=" O PHE X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 97 removed outlier: 3.649A pdb=" N SER X 88 " --> pdb=" O TYR X 84 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS X 97 " --> pdb=" O LEU X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 153 removed outlier: 4.261A pdb=" N GLY X 147 " --> pdb=" O GLU X 143 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET X 148 " --> pdb=" O GLN X 144 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER X 151 " --> pdb=" O GLY X 147 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU X 152 " --> pdb=" O MET X 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 175 removed outlier: 3.506A pdb=" N GLU X 164 " --> pdb=" O ASP X 160 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 72 removed outlier: 3.627A pdb=" N GLN Y 55 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU Y 58 " --> pdb=" O VAL Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 90 removed outlier: 3.769A pdb=" N ASN Y 87 " --> pdb=" O PHE Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 147 removed outlier: 4.651A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 170 removed outlier: 3.527A pdb=" N GLN Y 168 " --> pdb=" O LEU Y 164 " (cutoff:3.500A) removed outlier: 3.557A 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 GLN Z 62 " --> pdb=" O LEU Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 89 removed outlier: 3.981A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 3.556A pdb=" N ALA Z 135 " --> pdb=" O GLY Z 131 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY Z 142 " --> pdb=" O VAL Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 removed outlier: 3.641A pdb=" N ASP Z 154 " --> pdb=" O GLU Z 150 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE Z 160 " --> pdb=" O ALA Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 191 through 199 removed outlier: 4.240A pdb=" N GLU Z 197 " --> pdb=" O ALA Z 193 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS Z 198 " --> pdb=" O ASP Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 80 removed outlier: 3.831A pdb=" N LYS a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 99 removed outlier: 3.538A pdb=" N SER a 93 " --> pdb=" O ALA a 89 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR a 94 " --> pdb=" O ALA a 90 " (cutoff:3.500A) removed outlier: 3.744A 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: 3.513A pdb=" N MET a 172 " --> pdb=" O LEU a 168 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE a 180 " --> pdb=" O LYS a 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER a 181 " --> pdb=" O ASP a 177 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG a 185 " --> pdb=" O SER a 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 78 removed outlier: 3.543A pdb=" N ILE b 72 " --> pdb=" O GLY b 68 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU b 77 " --> pdb=" O ASP b 73 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 102 removed outlier: 3.753A pdb=" N ARG b 100 " --> pdb=" O MET b 96 " (cutoff:3.500A) removed outlier: 3.729A 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: 3.830A pdb=" N LYS b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 5.847A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 52 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 216 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 removed outlier: 4.567A 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: 3.575A pdb=" N GLY B 36 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 34 " --> pdb=" O MET B 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN B 213 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.617A pdb=" N ILE B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.538A 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 77 removed outlier: 3.637A pdb=" N SER C 75 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.592A 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: 3.635A pdb=" N VAL D 41 " --> pdb=" O MET D 211 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL D 210 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 3.503A 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: 4.165A pdb=" N LEU E 153 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 3.696A 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: 3.854A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB5, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB6, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB7, first strand: chain 'G' and resid 66 through 68 Processing sheet with id=AB8, first strand: chain 'H' and resid 125 through 128 removed outlier: 3.590A pdb=" N GLY H 11 " --> pdb=" O PHE H 8 " (cutoff:3.500A) removed outlier: 3.853A 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: 6.088A pdb=" N THR H 22 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 5.038A 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: 3.535A pdb=" N ALA H 101 " --> pdb=" O PHE H 42 " (cutoff:3.500A) removed outlier: 3.608A 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: 7.622A pdb=" N ILE I 173 " --> pdb=" O PRO I 188 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 20 through 22 removed outlier: 5.770A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.694A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA I 97 " --> pdb=" O ALA I 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 213 through 218 removed outlier: 3.537A pdb=" N THR I 213 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 6.218A 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: 6.131A 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: 3.643A pdb=" N LEU K 4 " --> pdb=" O HIS K 132 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL K 15 " --> pdb=" O ARG K 181 " (cutoff:3.500A) removed outlier: 3.506A 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: 3.905A pdb=" N MET K 118 " --> pdb=" O LEU K 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.861A pdb=" N SER L 188 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N HIS L 178 " --> pdb=" O ARG L 186 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 22 removed outlier: 7.168A 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: 6.849A pdb=" N LEU L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR L 44 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 3.727A 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: 5.751A 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: 7.048A pdb=" N LEU M 29 " --> pdb=" O HIS M 36 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU M 31 " --> pdb=" O SER M 34 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 43 through 45 removed outlier: 3.831A pdb=" N ASN M 108 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 3.759A 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: 3.543A pdb=" N GLY N 55 " --> pdb=" O GLY N 8 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 7 through 8 removed outlier: 3.543A pdb=" N GLY N 55 " --> pdb=" O GLY N 8 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 14 through 16 removed outlier: 3.531A pdb=" N GLY N 19 " --> pdb=" O PHE N 16 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE N 187 " --> pdb=" O PRO N 202 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE N 189 " --> pdb=" O GLU N 200 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.848A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR O 52 " --> pdb=" O GLU O 216 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU O 216 " --> pdb=" O THR O 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 69 through 71 removed outlier: 4.566A 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: 3.575A pdb=" N GLY P 36 " --> pdb=" O THR P 160 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER P 34 " --> pdb=" O MET P 162 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN P 213 " --> pdb=" O GLY P 216 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 65 through 68 removed outlier: 6.616A pdb=" N ILE P 71 " --> pdb=" O ILE P 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 161 through 164 removed outlier: 3.538A 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 77 removed outlier: 3.638A pdb=" N SER Q 75 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 10 through 11 removed outlier: 3.591A 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: 3.635A pdb=" N VAL R 41 " --> pdb=" O MET R 211 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL R 210 " --> pdb=" O LYS R 218 " (cutoff:3.500A) removed outlier: 3.503A 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: 4.165A pdb=" N LEU S 153 " --> pdb=" O CYS S 165 " (cutoff:3.500A) removed outlier: 3.697A 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: 3.854A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 63 through 65 Processing sheet with id=AF4, first strand: chain 'T' and resid 63 through 65 Processing sheet with id=AF5, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AF6, first strand: chain 'U' and resid 66 through 68 Processing sheet with id=AF7, first strand: chain 'V' and resid 125 through 128 removed outlier: 3.590A pdb=" N GLY V 11 " --> pdb=" O PHE V 8 " (cutoff:3.500A) removed outlier: 3.853A 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: 6.088A pdb=" N THR V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.037A 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: 3.535A pdb=" N ALA V 101 " --> pdb=" O PHE V 42 " (cutoff:3.500A) removed outlier: 3.608A 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: 7.617A pdb=" N ILE W 173 " --> pdb=" O PRO W 188 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 20 through 22 removed outlier: 5.770A pdb=" N GLU W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL W 26 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.694A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA W 97 " --> pdb=" O ALA W 46 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 213 through 218 removed outlier: 3.536A pdb=" N THR W 213 " --> pdb=" O THR X 198 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 6.218A 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: 6.132A 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: 3.643A pdb=" N LEU Y 4 " --> pdb=" O HIS Y 132 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL Y 15 " --> pdb=" O ARG Y 181 " (cutoff:3.500A) removed outlier: 3.506A 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: 3.905A pdb=" N MET Y 118 " --> pdb=" O LEU Y 102 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 125 through 129 removed outlier: 3.860A pdb=" N SER Z 188 " --> pdb=" O LEU Z 176 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N HIS Z 178 " --> pdb=" O ARG Z 186 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 20 through 22 removed outlier: 7.168A 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: 6.849A pdb=" N LEU Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR Z 44 " --> pdb=" O MET Z 100 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 3.726A 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: 5.752A 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: 7.047A pdb=" N LEU a 29 " --> pdb=" O HIS a 36 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU a 31 " --> pdb=" O SER a 34 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 43 through 45 removed outlier: 3.830A pdb=" N ASN a 108 " --> pdb=" O PHE a 124 " (cutoff:3.500A) removed outlier: 3.759A 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: 3.544A pdb=" N GLY b 55 " --> pdb=" O GLY b 8 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR b 49 " --> pdb=" O VAL b 45 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 7 through 8 removed outlier: 3.544A pdb=" N GLY b 55 " --> pdb=" O GLY b 8 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 14 through 16 removed outlier: 3.532A pdb=" N GLY b 19 " --> pdb=" O PHE b 16 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE b 187 " --> pdb=" O PRO b 202 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE b 189 " --> pdb=" O GLU b 200 " (cutoff:3.500A) 2438 hydrogen bonds defined for protein. 6927 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: 21.29 Time building geometry restraints manager: 17.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12846 1.33 - 1.45: 7337 1.45 - 1.57: 25523 1.57 - 1.69: 0 1.69 - 1.81: 462 Bond restraints: 46168 Sorted by residual: bond pdb=" CA GLN O 24 " pdb=" C GLN O 24 " ideal model delta sigma weight residual 1.523 1.497 0.027 1.30e-02 5.92e+03 4.16e+00 bond pdb=" N GLN O 24 " pdb=" CA GLN O 24 " ideal model delta sigma weight residual 1.459 1.437 0.022 1.21e-02 6.83e+03 3.35e+00 bond pdb=" N GLN D 215 " pdb=" CA GLN D 215 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.05e+00 bond pdb=" C SER B 15 " pdb=" O SER B 15 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.33e-02 5.65e+03 2.84e+00 bond pdb=" C GLN O 24 " pdb=" O GLN O 24 " ideal model delta sigma weight residual 1.237 1.219 0.017 1.17e-02 7.31e+03 2.21e+00 ... (remaining 46163 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.21: 1031 106.21 - 113.15: 25068 113.15 - 120.10: 15942 120.10 - 127.04: 20298 127.04 - 133.98: 350 Bond angle restraints: 62689 Sorted by residual: angle pdb=" N SER D 216 " pdb=" CA SER D 216 " pdb=" C SER D 216 " ideal model delta sigma weight residual 110.33 118.92 -8.59 1.29e+00 6.01e-01 4.43e+01 angle pdb=" N ASP A 10 " pdb=" CA ASP A 10 " pdb=" C ASP A 10 " ideal model delta sigma weight residual 111.28 106.23 5.05 1.09e+00 8.42e-01 2.15e+01 angle pdb=" N HIS O 12 " pdb=" CA HIS O 12 " pdb=" C HIS O 12 " ideal model delta sigma weight residual 111.36 115.86 -4.50 1.09e+00 8.42e-01 1.70e+01 angle pdb=" C GLN J 30 " pdb=" N ALA J 31 " pdb=" CA ALA J 31 " ideal model delta sigma weight residual 122.95 117.04 5.91 1.44e+00 4.82e-01 1.68e+01 angle pdb=" C GLN X 30 " pdb=" N ALA X 31 " pdb=" CA ALA X 31 " ideal model delta sigma weight residual 122.95 117.04 5.91 1.44e+00 4.82e-01 1.68e+01 ... (remaining 62684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 26832 16.05 - 32.09: 421 32.09 - 48.14: 123 48.14 - 64.18: 11 64.18 - 80.23: 22 Dihedral angle restraints: 27409 sinusoidal: 9534 harmonic: 17875 Sorted by residual: dihedral pdb=" CA ASN K 24 " pdb=" C ASN K 24 " pdb=" N ILE K 25 " pdb=" CA ILE K 25 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASN Y 24 " pdb=" C ASN Y 24 " pdb=" N ILE Y 25 " pdb=" CA ILE Y 25 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 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 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 27406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 6025 0.055 - 0.109: 1149 0.109 - 0.164: 160 0.164 - 0.219: 7 0.219 - 0.273: 3 Chirality restraints: 7344 Sorted by residual: chirality pdb=" CA GLN D 215 " pdb=" N GLN D 215 " pdb=" C GLN D 215 " pdb=" CB GLN D 215 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+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 2.28 0.23 2.00e-01 2.50e+01 1.36e+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 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 7341 not shown) Planarity restraints: 7971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 183 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.15e+00 pdb=" C VAL A 183 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL A 183 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS A 184 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL O 183 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C VAL O 183 " 0.046 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 O 17 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO O 18 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO O 18 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO O 18 " -0.031 5.00e-02 4.00e+02 ... (remaining 7968 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 1010 2.70 - 3.25: 43354 3.25 - 3.80: 69704 3.80 - 4.35: 94561 4.35 - 4.90: 160484 Nonbonded interactions: 369113 Sorted by model distance: nonbonded pdb=" O LYS M 49 " pdb=" OG1 THR M 50 " model vdw 2.144 2.440 nonbonded pdb=" O LYS a 49 " pdb=" OG1 THR a 50 " model vdw 2.144 2.440 nonbonded pdb=" OH TYR a 5 " pdb=" O PRO a 103 " model vdw 2.229 2.440 nonbonded pdb=" OH TYR M 5 " pdb=" O PRO M 103 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR D 31 " pdb=" O ARG D 163 " model vdw 2.233 2.440 ... (remaining 369108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 242) 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: 0.550 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: 4.860 Check model and map are aligned: 0.570 Set scattering table: 0.400 Process input model: 119.410 Find NCS groups from input model: 4.830 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 46168 Z= 0.170 Angle : 0.634 8.590 62689 Z= 0.408 Chirality : 0.044 0.273 7344 Planarity : 0.004 0.059 7971 Dihedral : 7.813 80.226 15997 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.95 % Rotamer: Outliers : 0.02 % Allowed : 0.37 % Favored : 99.60 % 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: -2.89 (0.09), residues: 6139 helix: -3.35 (0.07), residues: 2162 sheet: -0.87 (0.12), residues: 1470 loop : -0.91 (0.11), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 215 HIS 0.007 0.001 HIS G 72 PHE 0.020 0.001 PHE K 171 TYR 0.018 0.001 TYR V 136 ARG 0.005 0.000 ARG Z 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1782 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1781 time to evaluate : 3.643 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: A 86 ASP cc_start: 0.7132 (m-30) cc_final: 0.6522 (m-30) REVERT: B 70 HIS cc_start: 0.5995 (p-80) cc_final: 0.5710 (p-80) REVERT: B 71 ILE cc_start: 0.9049 (mt) cc_final: 0.8565 (mt) REVERT: B 94 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7436 (mm110) REVERT: C 6 ASP cc_start: 0.7582 (t0) cc_final: 0.7186 (t0) REVERT: D 110 TYR cc_start: 0.7905 (t80) cc_final: 0.7362 (t80) REVERT: E 13 ASN cc_start: 0.8643 (m-40) cc_final: 0.8338 (m-40) REVERT: G 81 LEU cc_start: 0.8248 (tp) cc_final: 0.7825 (tp) REVERT: G 118 TYR cc_start: 0.7407 (t80) cc_final: 0.7180 (t80) REVERT: H 53 GLN cc_start: 0.7977 (mt0) cc_final: 0.7527 (mt0) REVERT: I 209 THR cc_start: 0.7671 (m) cc_final: 0.7339 (t) REVERT: J 4 SER cc_start: 0.8318 (p) cc_final: 0.8067 (t) REVERT: J 192 ASP cc_start: 0.7304 (p0) cc_final: 0.6943 (p0) REVERT: K 62 LYS cc_start: 0.8355 (ttpp) cc_final: 0.8133 (tttm) REVERT: K 63 ASN cc_start: 0.8178 (m110) cc_final: 0.7882 (m-40) REVERT: K 87 ASN cc_start: 0.7739 (p0) cc_final: 0.7264 (p0) REVERT: K 90 ASP cc_start: 0.7162 (p0) cc_final: 0.6891 (p0) REVERT: K 101 ASN cc_start: 0.7281 (m110) cc_final: 0.7079 (m-40) REVERT: K 139 THR cc_start: 0.8482 (p) cc_final: 0.8107 (p) REVERT: L 33 LYS cc_start: 0.8335 (mttt) cc_final: 0.8081 (mttt) REVERT: M 91 MET cc_start: 0.7716 (ttp) cc_final: 0.7372 (ttm) REVERT: O 39 SER cc_start: 0.8419 (m) cc_final: 0.8207 (m) REVERT: P 57 ASP cc_start: 0.6948 (t0) cc_final: 0.6629 (t0) REVERT: Q 107 CYS cc_start: 0.7361 (m) cc_final: 0.6910 (m) REVERT: R 110 TYR cc_start: 0.7834 (t80) cc_final: 0.6903 (t80) REVERT: S 89 ILE cc_start: 0.8541 (pt) cc_final: 0.8210 (mt) REVERT: T 147 THR cc_start: 0.8187 (p) cc_final: 0.7985 (m) REVERT: V 90 TYR cc_start: 0.7476 (m-80) cc_final: 0.7118 (m-80) REVERT: V 99 ILE cc_start: 0.8926 (tt) cc_final: 0.8600 (mt) REVERT: W 53 ASP cc_start: 0.6460 (m-30) cc_final: 0.6189 (m-30) REVERT: X 164 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6615 (mm-30) REVERT: X 180 SER cc_start: 0.8475 (m) cc_final: 0.7747 (m) REVERT: Y 61 GLN cc_start: 0.7678 (tt0) cc_final: 0.6476 (tt0) REVERT: Y 62 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8117 (tttp) REVERT: Y 90 ASP cc_start: 0.7314 (p0) cc_final: 0.7058 (p0) REVERT: Y 108 ASP cc_start: 0.6930 (t0) cc_final: 0.5031 (t0) REVERT: Y 177 THR cc_start: 0.7623 (p) cc_final: 0.7101 (p) REVERT: a 75 TYR cc_start: 0.8328 (t80) cc_final: 0.7921 (t80) outliers start: 1 outliers final: 0 residues processed: 1782 average time/residue: 0.6116 time to fit residues: 1705.4681 Evaluate side-chains 1098 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1098 time to evaluate : 3.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 513 optimal weight: 3.9990 chunk 460 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 476 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 289 optimal weight: 1.9990 chunk 354 optimal weight: 4.9990 chunk 552 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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: