Starting phenix.real_space_refine on Mon Mar 25 01:06:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5m_31727/03_2024/7v5m_31727.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5m_31727/03_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_31727/03_2024/7v5m_31727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5m_31727/03_2024/7v5m_31727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5m_31727/03_2024/7v5m_31727.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5m_31727/03_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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 22.80, per 1000 atoms: 0.50 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: 16.35 Conformation dependent library (CDL) restraints added in 8.3 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: 5.45 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: 18.46 Time building geometry restraints manager: 17.71 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 4.560 Check model and map are aligned: 0.670 Set scattering table: 0.400 Process input model: 113.950 Find NCS groups from input model: 4.720 Set up NCS constraints: 0.500 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: 0.020 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.220 ------------------------------------------------------------------------------- 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 : 5.574 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: 0.4867 (p0) REVERT: Y 62 LYS cc_start: 0.8304 (ttpp) cc_final: 0.7965 (tttp) REVERT: Z 65 ILE cc_start: 0.7823 (mt) cc_final: 0.6705 (mt) REVERT: Z 85 ASN cc_start: 0.7116 (m-40) cc_final: 0.6471 (m-40) REVERT: Z 90 TYR cc_start: 0.5833 (m-80) cc_final: 0.5523 (m-80) REVERT: a 12 ILE cc_start: 0.7551 (pt) cc_final: 0.7144 (pt) REVERT: a 50 THR cc_start: 0.7231 (m) cc_final: 0.6997 (t) REVERT: a 168 LEU cc_start: 0.7669 (tp) cc_final: 0.7400 (tp) REVERT: b 59 ASP cc_start: 0.5519 (m-30) cc_final: 0.5296 (m-30) outliers start: 0 outliers final: 0 residues processed: 1951 average time/residue: 0.6220 time to fit residues: 1934.5988 Evaluate side-chains 1081 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1081 time to evaluate : 5.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 515 optimal weight: 0.9980 chunk 462 optimal weight: 5.9990 chunk 256 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 311 optimal weight: 0.1980 chunk 247 optimal weight: 9.9990 chunk 478 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 355 optimal weight: 0.0870 chunk 553 optimal weight: 5.9990 overall best weight: 2.0562 ------------------------------------------------------------------------------- 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 : 5.435 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: 0.5593 time to fit residues: 1162.7203 Evaluate side-chains 1052 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 960 time to evaluate : 4.708 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 120 GLN D 122 ASN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN F 21 GLN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 GLN K 189 HIS L 85 ASN M 8 ASN ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 GLN O 238 HIS ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 164 GLN S 182 GLN ** S 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 HIS ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 189 HIS Z 10 HIS Z 175 ASN a 152 GLN ** a 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 61 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.7183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 46182 Z= 0.458 Angle : 0.829 12.814 62708 Z= 0.436 Chirality : 0.049 0.227 7346 Planarity : 0.006 0.076 7974 Dihedral : 5.354 28.434 6788 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 5.32 % Allowed : 16.52 % Favored : 78.16 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.10), residues: 6142 helix: -0.03 (0.10), residues: 2228 sheet: -0.46 (0.12), residues: 1508 loop : -0.50 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP Q 159 HIS 0.016 0.002 HIS E 99 PHE 0.038 0.003 PHE A 191 TYR 0.033 0.003 TYR A 23 ARG 0.012 0.001 ARG Z 69 *********************** REFINEMENT MACRO_CYCLE 3 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 1200 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 973 time to evaluate : 5.128 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: A 114 LEU cc_start: 0.8756 (tp) cc_final: 0.8541 (tp) REVERT: A 140 LEU cc_start: 0.8363 (mt) cc_final: 0.8117 (mt) REVERT: B 94 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7628 (mm110) REVERT: B 101 GLN cc_start: 0.7591 (mm110) cc_final: 0.7376 (mm110) REVERT: B 112 ARG cc_start: 0.8361 (mtt90) cc_final: 0.8154 (mmt90) REVERT: B 117 MET cc_start: 0.7783 (ttm) cc_final: 0.7528 (ttp) REVERT: B 162 MET cc_start: 0.8043 (ptt) cc_final: 0.7645 (ptt) REVERT: C 98 LEU cc_start: 0.8541 (mp) cc_final: 0.8248 (tt) REVERT: C 114 LEU cc_start: 0.8751 (tp) cc_final: 0.8430 (tp) REVERT: D 124 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7527 (ttp-110) REVERT: D 190 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8450 (tp) REVERT: E 125 GLU cc_start: 0.7771 (pm20) cc_final: 0.7557 (pm20) REVERT: E 203 LYS cc_start: 0.8516 (pttm) cc_final: 0.8253 (ttpp) REVERT: E 216 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6402 (tt0) REVERT: G 158 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6694 (m-10) REVERT: H 57 ASP cc_start: 0.6567 (OUTLIER) cc_final: 0.6326 (t70) REVERT: H 133 SER cc_start: 0.7948 (p) cc_final: 0.7582 (t) REVERT: I 10 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6450 (p0) REVERT: K 38 MET cc_start: 0.7590 (mmm) cc_final: 0.7241 (tpp) REVERT: K 163 CYS cc_start: 0.7427 (m) cc_final: 0.7208 (m) REVERT: M 83 MET cc_start: 0.8952 (tpp) cc_final: 0.8647 (tpp) REVERT: M 122 TYR cc_start: 0.8722 (m-80) cc_final: 0.8420 (m-80) REVERT: N 76 LEU cc_start: 0.8274 (mt) cc_final: 0.7953 (mt) REVERT: O 88 ARG cc_start: 0.7923 (mmm160) cc_final: 0.7613 (tpt90) REVERT: P 9 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8057 (mp) REVERT: P 102 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7071 (tm-30) REVERT: Q 30 HIS cc_start: 0.7215 (m-70) cc_final: 0.6396 (m-70) REVERT: R 90 GLU cc_start: 0.8114 (tp30) cc_final: 0.7826 (tp30) REVERT: R 106 TYR cc_start: 0.7699 (t80) cc_final: 0.7274 (t80) REVERT: R 190 LEU cc_start: 0.8860 (mt) cc_final: 0.8645 (tp) REVERT: S 60 GLU cc_start: 0.6598 (tp30) cc_final: 0.6386 (tm-30) REVERT: S 89 ILE cc_start: 0.8813 (pt) cc_final: 0.8414 (mt) REVERT: T 108 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8687 (tt) REVERT: U 47 PHE cc_start: 0.7513 (m-80) cc_final: 0.7280 (m-80) REVERT: V 51 ASP cc_start: 0.6896 (m-30) cc_final: 0.6552 (m-30) REVERT: V 95 MET cc_start: 0.7815 (tmm) cc_final: 0.7571 (tmm) REVERT: V 133 SER cc_start: 0.8071 (p) cc_final: 0.7769 (t) REVERT: W 37 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7520 (mt) REVERT: X 3 MET cc_start: 0.7573 (mmm) cc_final: 0.7275 (mmm) REVERT: X 71 ASN cc_start: 0.8005 (m-40) cc_final: 0.7766 (m110) REVERT: X 192 ASP cc_start: 0.7090 (p0) cc_final: 0.6888 (p0) REVERT: Y 11 ASP cc_start: 0.6425 (p0) cc_final: 0.6178 (p0) REVERT: Y 29 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8498 (tptm) REVERT: Y 87 ASN cc_start: 0.7762 (p0) cc_final: 0.7267 (p0) REVERT: Y 139 THR cc_start: 0.8872 (m) cc_final: 0.7576 (m) REVERT: Z 30 THR cc_start: 0.7499 (t) cc_final: 0.7123 (t) REVERT: Z 45 MET cc_start: 0.6982 (mmm) cc_final: 0.6320 (mtp) REVERT: a 83 MET cc_start: 0.8850 (tpp) cc_final: 0.8426 (tpp) REVERT: a 130 TYR cc_start: 0.7776 (t80) cc_final: 0.7427 (t80) REVERT: a 205 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: b 76 LEU cc_start: 0.8401 (mt) cc_final: 0.8128 (mt) REVERT: b 170 GLU cc_start: 0.7867 (pp20) cc_final: 0.7156 (pp20) outliers start: 227 outliers final: 113 residues processed: 1121 average time/residue: 0.5710 time to fit residues: 1044.6167 Evaluate side-chains 905 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 781 time to evaluate : 6.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 221 ASN Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 144 ARG Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 186 ARG Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 130 TYR Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 160 TYR Chi-restraints excluded: chain O residue 161 CYS Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain S residue 195 ILE Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 206 ASP Chi-restraints excluded: chain U residue 221 ASN Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 170 SER Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 10 ASP Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 69 ARG Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 146 TYR Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 157 VAL Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Z residue 93 MET Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 205 GLU Chi-restraints excluded: chain b residue 50 MET Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 98 SER Chi-restraints excluded: chain b residue 101 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 548 optimal weight: 3.9990 chunk 417 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 264 optimal weight: 0.9990 chunk 372 optimal weight: 0.9980 chunk 556 optimal weight: 5.9990 chunk 589 optimal weight: 7.9990 chunk 290 optimal weight: 0.8980 chunk 527 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 193 GLN B 108 GLN D 54 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 HIS N 108 ASN P 20 GLN P 101 GLN P 111 GLN ** Q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 23 GLN ** S 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 180 GLN ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 66 HIS W 80 ASN W 85 GLN X 32 GLN ** Z 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN ** a 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 108 ASN b 147 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.7451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 46182 Z= 0.219 Angle : 0.647 9.017 62708 Z= 0.335 Chirality : 0.044 0.224 7346 Planarity : 0.004 0.049 7974 Dihedral : 4.821 27.026 6788 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.37 % Allowed : 19.49 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.10), residues: 6142 helix: 0.48 (0.11), residues: 2244 sheet: -0.27 (0.13), residues: 1508 loop : -0.36 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 103 HIS 0.008 0.001 HIS E 99 PHE 0.025 0.002 PHE F 87 TYR 0.032 0.002 TYR C 136 ARG 0.009 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 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 1055 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 911 time to evaluate : 4.425 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: B 109 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8747 (tp) REVERT: B 111 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: B 162 MET cc_start: 0.8261 (ptt) cc_final: 0.7886 (ptt) REVERT: B 191 ILE cc_start: 0.8846 (pt) cc_final: 0.8563 (mt) REVERT: C 98 LEU cc_start: 0.8505 (mp) cc_final: 0.8145 (tt) REVERT: D 192 ILE cc_start: 0.9103 (pt) cc_final: 0.8853 (mt) REVERT: E 182 GLN cc_start: 0.7661 (pp30) cc_final: 0.6822 (pp30) REVERT: I 10 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6594 (p0) REVERT: I 126 THR cc_start: 0.8983 (p) cc_final: 0.8725 (p) REVERT: I 135 MET cc_start: 0.7894 (tpp) cc_final: 0.7659 (tpp) REVERT: J 146 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6713 (t80) REVERT: J 162 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8502 (tt) REVERT: J 203 MET cc_start: 0.8152 (mmm) cc_final: 0.7730 (mmp) REVERT: K 18 ASP cc_start: 0.8351 (t0) cc_final: 0.8044 (t70) REVERT: K 165 GLU cc_start: 0.7110 (tm-30) cc_final: 0.5923 (tm-30) REVERT: M 83 MET cc_start: 0.8585 (tpp) cc_final: 0.8206 (tpp) REVERT: M 122 TYR cc_start: 0.8665 (m-80) cc_final: 0.8408 (m-80) REVERT: N 76 LEU cc_start: 0.8146 (mt) cc_final: 0.7825 (mt) REVERT: Q 30 HIS cc_start: 0.6812 (m-70) cc_final: 0.6544 (m-70) REVERT: Q 68 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7806 (mt) REVERT: R 106 TYR cc_start: 0.7513 (t80) cc_final: 0.7096 (t80) REVERT: S 89 ILE cc_start: 0.8718 (pt) cc_final: 0.8392 (mt) REVERT: T 108 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8721 (tt) REVERT: V 51 ASP cc_start: 0.6734 (m-30) cc_final: 0.6500 (m-30) REVERT: V 90 TYR cc_start: 0.7356 (m-80) cc_final: 0.6688 (m-80) REVERT: V 133 SER cc_start: 0.8007 (p) cc_final: 0.7784 (t) REVERT: W 94 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8525 (pt) REVERT: X 102 TYR cc_start: 0.8440 (m-80) cc_final: 0.8032 (m-10) REVERT: Y 11 ASP cc_start: 0.6259 (p0) cc_final: 0.5947 (p0) REVERT: Y 29 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8366 (tptm) REVERT: Z 45 MET cc_start: 0.6638 (mmm) cc_final: 0.5643 (ttt) REVERT: Z 139 MET cc_start: 0.7344 (tmm) cc_final: 0.6916 (tmm) REVERT: a 114 ASP cc_start: 0.8152 (p0) cc_final: 0.7941 (p0) REVERT: b 76 LEU cc_start: 0.8448 (mt) cc_final: 0.8119 (mt) REVERT: b 96 MET cc_start: 0.7433 (tpp) cc_final: 0.6958 (tpp) REVERT: b 168 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7745 (mm) REVERT: b 170 GLU cc_start: 0.7804 (pp20) cc_final: 0.7433 (pp20) outliers start: 144 outliers final: 80 residues processed: 1000 average time/residue: 0.5748 time to fit residues: 938.7717 Evaluate side-chains 877 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 787 time to evaluate : 5.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain U residue 206 ASP Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 10 ASP Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 60 GLN Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 105 GLU Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 143 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 491 optimal weight: 5.9990 chunk 334 optimal weight: 30.0000 chunk 8 optimal weight: 0.9980 chunk 439 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 503 optimal weight: 4.9990 chunk 407 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 301 optimal weight: 8.9990 chunk 529 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN C 230 GLN D 120 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN H 62 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN P 101 GLN P 111 GLN Q 40 ASN ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN R 120 GLN S 23 GLN ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 GLN ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 ASN X 92 ASN X 156 ASN Y 110 HIS a 8 ASN ** a 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 108 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.7962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 46182 Z= 0.300 Angle : 0.659 9.692 62708 Z= 0.343 Chirality : 0.044 0.191 7346 Planarity : 0.004 0.049 7974 Dihedral : 4.767 26.882 6788 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.69 % Allowed : 19.28 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.10), residues: 6142 helix: 0.65 (0.11), residues: 2232 sheet: -0.30 (0.13), residues: 1516 loop : -0.27 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 107 HIS 0.007 0.001 HIS E 99 PHE 0.021 0.002 PHE Y 83 TYR 0.029 0.002 TYR C 136 ARG 0.010 0.001 ARG V 89 *********************** REFINEMENT MACRO_CYCLE 5 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 1023 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 823 time to evaluate : 5.092 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: B 112 ARG cc_start: 0.8537 (mtt90) cc_final: 0.7948 (mmt90) REVERT: B 191 ILE cc_start: 0.8879 (pt) cc_final: 0.8573 (mt) REVERT: C 98 LEU cc_start: 0.8527 (mp) cc_final: 0.8162 (tt) REVERT: D 73 PHE cc_start: 0.7818 (p90) cc_final: 0.7616 (p90) REVERT: E 182 GLN cc_start: 0.7544 (pp30) cc_final: 0.6678 (pp30) REVERT: F 9 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6581 (m-30) REVERT: F 61 LYS cc_start: 0.8595 (ptmm) cc_final: 0.8320 (tttt) REVERT: G 158 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6751 (m-10) REVERT: H 147 MET cc_start: 0.7104 (mmt) cc_final: 0.6594 (mmt) REVERT: I 10 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6723 (p0) REVERT: J 146 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.7025 (t80) REVERT: J 162 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8662 (tt) REVERT: J 203 MET cc_start: 0.8274 (mmm) cc_final: 0.8070 (mmp) REVERT: M 83 MET cc_start: 0.8429 (tpp) cc_final: 0.8198 (tpp) REVERT: M 166 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7202 (mp) REVERT: N 76 LEU cc_start: 0.8233 (mt) cc_final: 0.7987 (mt) REVERT: Q 68 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7819 (mt) REVERT: R 106 TYR cc_start: 0.7632 (t80) cc_final: 0.7393 (t80) REVERT: S 89 ILE cc_start: 0.8831 (pt) cc_final: 0.8460 (mt) REVERT: V 51 ASP cc_start: 0.7029 (m-30) cc_final: 0.6781 (m-30) REVERT: X 3 MET cc_start: 0.7684 (mmm) cc_final: 0.7422 (mmm) REVERT: X 58 ASP cc_start: 0.7166 (m-30) cc_final: 0.6743 (m-30) REVERT: X 67 LYS cc_start: 0.8409 (mmmm) cc_final: 0.8144 (tppp) REVERT: X 117 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7688 (tppt) REVERT: Y 11 ASP cc_start: 0.6394 (p0) cc_final: 0.6025 (p0) REVERT: Y 29 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8558 (tptm) REVERT: Y 118 MET cc_start: 0.7629 (ttp) cc_final: 0.7412 (ttm) REVERT: Z 45 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6294 (ttm) REVERT: Z 139 MET cc_start: 0.7507 (tmm) cc_final: 0.7238 (tmm) REVERT: a 75 TYR cc_start: 0.8464 (t80) cc_final: 0.8246 (t80) REVERT: a 114 ASP cc_start: 0.8332 (p0) cc_final: 0.8116 (p0) REVERT: b 79 ASP cc_start: 0.7462 (p0) cc_final: 0.7047 (p0) REVERT: b 168 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7986 (mm) REVERT: b 170 GLU cc_start: 0.7699 (pp20) cc_final: 0.7395 (pp20) outliers start: 200 outliers final: 118 residues processed: 953 average time/residue: 0.6152 time to fit residues: 976.6026 Evaluate side-chains 885 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 757 time to evaluate : 7.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 96 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 160 TYR Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 47 CYS Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 206 ASP Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 10 ASP Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 60 GLN Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 105 GLU Chi-restraints excluded: chain X residue 146 TYR Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 143 LEU Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 45 MET Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 198 optimal weight: 20.0000 chunk 530 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 346 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 590 optimal weight: 1.9990 chunk 489 optimal weight: 10.0000 chunk 273 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 195 optimal weight: 8.9990 chunk 309 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 108 GLN C 230 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 GLN O 92 GLN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 GLN P 111 GLN Q 40 ASN Q 119 GLN ** Q 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN ** a 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.8370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 46182 Z= 0.307 Angle : 0.668 10.912 62708 Z= 0.346 Chirality : 0.045 0.326 7346 Planarity : 0.004 0.050 7974 Dihedral : 4.765 27.346 6788 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.15 % Allowed : 20.34 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.11), residues: 6142 helix: 0.71 (0.11), residues: 2234 sheet: -0.28 (0.13), residues: 1466 loop : -0.29 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 104 HIS 0.007 0.001 HIS E 99 PHE 0.017 0.002 PHE A 191 TYR 0.037 0.002 TYR D 153 ARG 0.011 0.001 ARG V 89 *********************** REFINEMENT MACRO_CYCLE 6 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 964 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 787 time to evaluate : 5.002 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: B 118 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8297 (tm-30) REVERT: B 191 ILE cc_start: 0.8935 (pt) cc_final: 0.8698 (mt) REVERT: C 98 LEU cc_start: 0.8565 (mp) cc_final: 0.8209 (tt) REVERT: D 96 LEU cc_start: 0.8654 (tp) cc_final: 0.8443 (tp) REVERT: E 141 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7952 (mp) REVERT: E 182 GLN cc_start: 0.7559 (pp30) cc_final: 0.6848 (pp30) REVERT: E 228 MET cc_start: 0.7855 (tpt) cc_final: 0.7505 (tpt) REVERT: F 61 LYS cc_start: 0.8562 (ptmm) cc_final: 0.8323 (tttt) REVERT: G 158 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.6707 (m-10) REVERT: G 178 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7173 (ptmm) REVERT: H 147 MET cc_start: 0.6865 (mmt) cc_final: 0.6514 (mmt) REVERT: I 10 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6714 (p0) REVERT: I 135 MET cc_start: 0.7870 (tpp) cc_final: 0.7620 (tpp) REVERT: J 146 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.7264 (t80) REVERT: J 162 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8654 (tt) REVERT: J 203 MET cc_start: 0.8323 (mmm) cc_final: 0.8048 (mmp) REVERT: M 166 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7278 (mp) REVERT: N 76 LEU cc_start: 0.8293 (mt) cc_final: 0.8072 (mt) REVERT: Q 68 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7959 (mt) REVERT: R 106 TYR cc_start: 0.7795 (t80) cc_final: 0.7572 (t80) REVERT: S 89 ILE cc_start: 0.8821 (pt) cc_final: 0.8489 (mt) REVERT: V 100 ILE cc_start: 0.9120 (mp) cc_final: 0.8895 (mt) REVERT: X 58 ASP cc_start: 0.7109 (m-30) cc_final: 0.6834 (m-30) REVERT: X 67 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8301 (tppp) REVERT: X 97 LYS cc_start: 0.8314 (ptpp) cc_final: 0.7845 (ptpp) REVERT: X 102 TYR cc_start: 0.8461 (m-10) cc_final: 0.8074 (m-10) REVERT: X 117 LYS cc_start: 0.8279 (mmmt) cc_final: 0.8014 (tppt) REVERT: Y 11 ASP cc_start: 0.6599 (p0) cc_final: 0.6296 (p0) REVERT: Y 29 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8575 (tptm) REVERT: Z 45 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6409 (ttm) REVERT: Z 139 MET cc_start: 0.7532 (tmm) cc_final: 0.7201 (tmm) REVERT: a 75 TYR cc_start: 0.8558 (t80) cc_final: 0.8175 (t80) REVERT: a 83 MET cc_start: 0.8679 (tpp) cc_final: 0.8103 (tpp) REVERT: b 79 ASP cc_start: 0.7653 (p0) cc_final: 0.7360 (p0) REVERT: b 170 GLU cc_start: 0.7642 (pp20) cc_final: 0.7355 (pp20) outliers start: 177 outliers final: 119 residues processed: 906 average time/residue: 0.5703 time to fit residues: 850.0181 Evaluate side-chains 853 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 724 time to evaluate : 5.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 96 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 160 TYR Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 47 CYS Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 133 MET Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 75 MET Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 10 ASP Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 60 GLN Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 146 TYR Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 108 ASP Chi-restraints excluded: chain Y residue 143 LEU Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 45 MET Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 569 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 chunk 431 optimal weight: 5.9990 chunk 333 optimal weight: 5.9990 chunk 496 optimal weight: 0.5980 chunk 329 optimal weight: 10.0000 chunk 587 optimal weight: 8.9990 chunk 367 optimal weight: 0.7980 chunk 358 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN P 51 GLN P 111 GLN Q 40 ASN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 221 GLN ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN a 131 GLN ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.8531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 46182 Z= 0.214 Angle : 0.650 12.403 62708 Z= 0.334 Chirality : 0.044 0.285 7346 Planarity : 0.004 0.051 7974 Dihedral : 4.624 26.929 6788 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.63 % Allowed : 21.32 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 6142 helix: 0.85 (0.11), residues: 2222 sheet: -0.24 (0.13), residues: 1452 loop : -0.25 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 104 HIS 0.006 0.001 HIS E 99 PHE 0.021 0.001 PHE F 87 TYR 0.028 0.001 TYR D 153 ARG 0.010 0.000 ARG V 89 *********************** REFINEMENT MACRO_CYCLE 7 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 975 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 820 time to evaluate : 5.249 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: B 109 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8838 (tp) REVERT: C 98 LEU cc_start: 0.8541 (mp) cc_final: 0.8195 (tt) REVERT: E 141 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7985 (mp) REVERT: E 182 GLN cc_start: 0.7350 (pp30) cc_final: 0.6923 (pp30) REVERT: F 61 LYS cc_start: 0.8483 (ptmm) cc_final: 0.8261 (tttt) REVERT: G 158 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.6491 (m-10) REVERT: I 127 MET cc_start: 0.8010 (ptm) cc_final: 0.7783 (ptp) REVERT: I 182 LYS cc_start: 0.8155 (ptmm) cc_final: 0.7911 (ptmm) REVERT: J 11 MET cc_start: 0.8715 (tmm) cc_final: 0.8387 (tmm) REVERT: J 33 MET cc_start: 0.7888 (tmm) cc_final: 0.7553 (tmm) REVERT: J 79 ARG cc_start: 0.7414 (ttp80) cc_final: 0.7128 (ttp80) REVERT: J 146 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6967 (t80) REVERT: J 203 MET cc_start: 0.8375 (mmm) cc_final: 0.8154 (mmp) REVERT: L 100 MET cc_start: 0.7838 (mtt) cc_final: 0.7535 (mtt) REVERT: M 166 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7246 (mp) REVERT: N 76 LEU cc_start: 0.8239 (mt) cc_final: 0.8005 (mt) REVERT: Q 68 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7929 (mt) REVERT: Q 72 MET cc_start: 0.6347 (ptm) cc_final: 0.6059 (ptm) REVERT: S 84 ASP cc_start: 0.7183 (m-30) cc_final: 0.6916 (m-30) REVERT: S 89 ILE cc_start: 0.8800 (pt) cc_final: 0.8459 (mt) REVERT: V 100 ILE cc_start: 0.9062 (mp) cc_final: 0.8841 (mt) REVERT: X 67 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8314 (tppp) REVERT: X 97 LYS cc_start: 0.8254 (ptpp) cc_final: 0.7684 (ptpp) REVERT: X 102 TYR cc_start: 0.8373 (m-10) cc_final: 0.7901 (m-10) REVERT: X 117 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8098 (tppt) REVERT: Y 8 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7571 (tm-30) REVERT: Y 11 ASP cc_start: 0.6642 (p0) cc_final: 0.6380 (p0) REVERT: Y 29 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8649 (tptm) REVERT: Z 45 MET cc_start: 0.6412 (mmm) cc_final: 0.6069 (ttm) REVERT: Z 139 MET cc_start: 0.7467 (tmm) cc_final: 0.7168 (tmm) REVERT: a 75 TYR cc_start: 0.8558 (t80) cc_final: 0.8226 (t80) REVERT: a 83 MET cc_start: 0.8569 (tpp) cc_final: 0.8097 (tpp) REVERT: b 170 GLU cc_start: 0.7604 (pp20) cc_final: 0.7348 (pp20) REVERT: b 185 ASN cc_start: 0.7925 (t0) cc_final: 0.7429 (t0) outliers start: 155 outliers final: 100 residues processed: 931 average time/residue: 0.5716 time to fit residues: 873.0620 Evaluate side-chains 865 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 758 time to evaluate : 4.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 89 ARG Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 96 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 133 MET Chi-restraints excluded: chain S residue 204 GLN Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 75 MET Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 10 ASP Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 60 GLN Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 146 TYR Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 363 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 351 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 113 optimal weight: 0.3980 chunk 373 optimal weight: 4.9990 chunk 400 optimal weight: 20.0000 chunk 290 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 462 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 GLN P 20 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN Q 40 ASN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN a 131 GLN ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.8646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 46182 Z= 0.194 Angle : 0.656 12.782 62708 Z= 0.335 Chirality : 0.044 0.324 7346 Planarity : 0.004 0.054 7974 Dihedral : 4.551 26.431 6788 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.84 % Allowed : 22.28 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.11), residues: 6142 helix: 0.93 (0.11), residues: 2228 sheet: -0.15 (0.13), residues: 1432 loop : -0.24 (0.13), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 107 HIS 0.007 0.001 HIS E 99 PHE 0.022 0.001 PHE F 87 TYR 0.027 0.001 TYR D 110 ARG 0.011 0.000 ARG W 89 *********************** REFINEMENT MACRO_CYCLE 8 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 940 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 819 time to evaluate : 6.055 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: B 109 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8873 (tp) REVERT: C 98 LEU cc_start: 0.8566 (mp) cc_final: 0.8202 (tt) REVERT: E 182 GLN cc_start: 0.7466 (pp30) cc_final: 0.7151 (pp30) REVERT: F 61 LYS cc_start: 0.8484 (ptmm) cc_final: 0.8279 (tttt) REVERT: H 93 ASP cc_start: 0.8629 (p0) cc_final: 0.8282 (p0) REVERT: J 33 MET cc_start: 0.7855 (tmm) cc_final: 0.7485 (tmm) REVERT: J 146 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6857 (t80) REVERT: J 203 MET cc_start: 0.8400 (mmm) cc_final: 0.8181 (mmp) REVERT: K 38 MET cc_start: 0.7683 (mmm) cc_final: 0.7446 (tpp) REVERT: L 100 MET cc_start: 0.7850 (mtt) cc_final: 0.7524 (mtt) REVERT: M 166 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7354 (mp) REVERT: N 76 LEU cc_start: 0.8248 (mt) cc_final: 0.8017 (mt) REVERT: O 114 LEU cc_start: 0.8793 (tp) cc_final: 0.8542 (tp) REVERT: Q 68 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7877 (mt) REVERT: Q 72 MET cc_start: 0.6187 (ptm) cc_final: 0.5895 (ptm) REVERT: S 84 ASP cc_start: 0.7191 (m-30) cc_final: 0.6967 (m-30) REVERT: S 89 ILE cc_start: 0.8809 (pt) cc_final: 0.8405 (mt) REVERT: U 108 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8253 (tt) REVERT: V 100 ILE cc_start: 0.9052 (mp) cc_final: 0.8816 (mt) REVERT: W 89 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7462 (ttp80) REVERT: W 146 MET cc_start: 0.5958 (mtt) cc_final: 0.5658 (mtt) REVERT: X 67 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8340 (tppp) REVERT: X 97 LYS cc_start: 0.8224 (ptpp) cc_final: 0.7642 (ptpp) REVERT: X 102 TYR cc_start: 0.8332 (m-10) cc_final: 0.7875 (m-10) REVERT: X 117 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8118 (tppt) REVERT: Y 8 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7713 (tm-30) REVERT: Y 11 ASP cc_start: 0.6544 (p0) cc_final: 0.6314 (p0) REVERT: Y 29 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8711 (tptm) REVERT: Y 38 MET cc_start: 0.6924 (tpp) cc_final: 0.6625 (mmm) REVERT: Z 45 MET cc_start: 0.6470 (mmm) cc_final: 0.6046 (ttm) REVERT: Z 139 MET cc_start: 0.7468 (tmm) cc_final: 0.7157 (tmm) REVERT: b 170 GLU cc_start: 0.7528 (pp20) cc_final: 0.7202 (pp20) REVERT: b 185 ASN cc_start: 0.7888 (t0) cc_final: 0.7427 (t0) outliers start: 121 outliers final: 94 residues processed: 892 average time/residue: 0.5561 time to fit residues: 816.7109 Evaluate side-chains 864 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 764 time to evaluate : 5.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 89 ARG Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 96 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 133 MET Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 75 MET Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 113 ASP Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 10 ASP Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 60 GLN Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 146 TYR Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 143 LEU Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 534 optimal weight: 9.9990 chunk 563 optimal weight: 10.0000 chunk 513 optimal weight: 10.0000 chunk 547 optimal weight: 7.9990 chunk 329 optimal weight: 20.0000 chunk 238 optimal weight: 0.8980 chunk 430 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 495 optimal weight: 2.9990 chunk 518 optimal weight: 9.9990 chunk 545 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 HIS ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 10 HIS ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN Q 40 ASN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 HIS ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 82 ASN b 65 GLN b 108 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.8877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 46182 Z= 0.277 Angle : 0.692 12.193 62708 Z= 0.355 Chirality : 0.045 0.324 7346 Planarity : 0.005 0.097 7974 Dihedral : 4.634 26.486 6788 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.12 % Allowed : 22.63 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 6142 helix: 0.89 (0.11), residues: 2214 sheet: -0.14 (0.13), residues: 1430 loop : -0.28 (0.13), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 215 HIS 0.012 0.001 HIS C 30 PHE 0.031 0.002 PHE K 83 TYR 0.039 0.002 TYR a 75 ARG 0.011 0.001 ARG W 89 *********************** REFINEMENT MACRO_CYCLE 9 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 915 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 782 time to evaluate : 5.383 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: A 80 MET cc_start: 0.8326 (mpp) cc_final: 0.8081 (mpp) REVERT: B 88 ARG cc_start: 0.7469 (mmm-85) cc_final: 0.7006 (mmm160) REVERT: B 111 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: C 98 LEU cc_start: 0.8574 (mp) cc_final: 0.8229 (tt) REVERT: E 182 GLN cc_start: 0.7529 (pp30) cc_final: 0.7251 (pp30) REVERT: F 61 LYS cc_start: 0.8511 (ptmm) cc_final: 0.8297 (tttt) REVERT: G 158 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.6831 (m-10) REVERT: G 178 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7334 (ptmm) REVERT: G 219 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7599 (pp) REVERT: H 93 ASP cc_start: 0.8695 (p0) cc_final: 0.8314 (p0) REVERT: I 80 ASN cc_start: 0.8007 (t0) cc_final: 0.7743 (t0) REVERT: J 33 MET cc_start: 0.7871 (tmm) cc_final: 0.7340 (tmm) REVERT: J 146 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.7075 (t80) REVERT: K 102 LEU cc_start: 0.8580 (mm) cc_final: 0.8335 (mp) REVERT: L 100 MET cc_start: 0.7829 (mtt) cc_final: 0.7548 (mtt) REVERT: M 166 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7348 (mp) REVERT: N 76 LEU cc_start: 0.8072 (mt) cc_final: 0.7806 (mt) REVERT: Q 68 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8018 (mt) REVERT: U 108 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8337 (tt) REVERT: V 37 ILE cc_start: 0.8440 (mp) cc_final: 0.8145 (mp) REVERT: V 100 ILE cc_start: 0.9060 (mp) cc_final: 0.8837 (mt) REVERT: W 146 MET cc_start: 0.6037 (mtt) cc_final: 0.5728 (mtt) REVERT: X 67 LYS cc_start: 0.8631 (mmmm) cc_final: 0.8395 (tppp) REVERT: X 97 LYS cc_start: 0.8286 (ptpp) cc_final: 0.7663 (ptpp) REVERT: X 102 TYR cc_start: 0.8312 (m-10) cc_final: 0.7875 (m-10) REVERT: X 117 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8202 (tppt) REVERT: Y 8 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7616 (tm-30) REVERT: Y 29 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8708 (tptm) REVERT: Z 45 MET cc_start: 0.6672 (mmm) cc_final: 0.6201 (ttm) REVERT: Z 139 MET cc_start: 0.7456 (tmm) cc_final: 0.7134 (tmm) REVERT: b 170 GLU cc_start: 0.7541 (pp20) cc_final: 0.7209 (pp20) REVERT: b 185 ASN cc_start: 0.7881 (t0) cc_final: 0.7358 (t0) outliers start: 133 outliers final: 104 residues processed: 864 average time/residue: 0.6181 time to fit residues: 881.1014 Evaluate side-chains 853 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 740 time to evaluate : 5.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR 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 C residue 64 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 89 ARG Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 96 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain S residue 47 CYS Chi-restraints excluded: chain S residue 118 ASN Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 133 MET Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 75 MET Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 113 ASP Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 133 SER Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 10 ASP Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 60 GLN Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 146 TYR Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 143 LEU Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 205 GLU Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 359 optimal weight: 0.0670 chunk 579 optimal weight: 6.9990 chunk 353 optimal weight: 10.0000 chunk 274 optimal weight: 0.8980 chunk 402 optimal weight: 6.9990 chunk 607 optimal weight: 8.9990 chunk 559 optimal weight: 9.9990 chunk 483 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 373 optimal weight: 6.9990 chunk 296 optimal weight: 9.9990 overall best weight: 4.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN ** P 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.8894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.340 46182 Z= 0.412 Angle : 0.795 59.198 62708 Z= 0.422 Chirality : 0.046 0.760 7346 Planarity : 0.005 0.092 7974 Dihedral : 4.636 26.486 6788 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.90 % Favored : 97.09 % Rotamer: Outliers : 3.05 % Allowed : 22.80 % Favored : 74.16 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.11), residues: 6142 helix: 0.86 (0.11), residues: 2216 sheet: -0.15 (0.13), residues: 1430 loop : -0.29 (0.13), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 215 HIS 0.009 0.001 HIS C 30 PHE 0.030 0.001 PHE K 83 TYR 0.042 0.002 TYR C 136 ARG 0.086 0.001 ARG R 125 ********************** REFINEMENT MACRO_CYCLE 10 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 872 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 742 time to evaluate : 5.311 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: B 88 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.7029 (mmm160) REVERT: B 111 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7129 (mp10) REVERT: C 98 LEU cc_start: 0.8571 (mp) cc_final: 0.8242 (tt) REVERT: E 182 GLN cc_start: 0.7558 (pp30) cc_final: 0.7252 (pp30) REVERT: G 158 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.6831 (m-10) REVERT: G 178 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7339 (ptmm) REVERT: G 219 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7595 (pp) REVERT: H 93 ASP cc_start: 0.8716 (p0) cc_final: 0.8303 (p0) REVERT: I 80 ASN cc_start: 0.8005 (t0) cc_final: 0.7757 (t0) REVERT: J 33 MET cc_start: 0.7910 (tmm) cc_final: 0.7391 (tmm) REVERT: J 146 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.7069 (t80) REVERT: J 203 MET cc_start: 0.8428 (mmm) cc_final: 0.8070 (mmp) REVERT: K 102 LEU cc_start: 0.8596 (mm) cc_final: 0.8339 (mp) REVERT: L 100 MET cc_start: 0.7821 (mtt) cc_final: 0.7532 (mtt) REVERT: M 166 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7346 (mp) REVERT: N 76 LEU cc_start: 0.8071 (mt) cc_final: 0.7799 (mt) REVERT: Q 68 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8022 (mt) REVERT: U 108 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8339 (tt) REVERT: V 37 ILE cc_start: 0.8430 (mp) cc_final: 0.8148 (mp) REVERT: V 100 ILE cc_start: 0.9055 (mp) cc_final: 0.8835 (mt) REVERT: W 89 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7534 (ttp80) REVERT: W 146 MET cc_start: 0.6041 (mtt) cc_final: 0.5733 (mtt) REVERT: X 58 ASP cc_start: 0.6665 (p0) cc_final: 0.6443 (p0) REVERT: X 67 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8396 (tppp) REVERT: X 97 LYS cc_start: 0.8283 (ptpp) cc_final: 0.7650 (ptpp) REVERT: X 102 TYR cc_start: 0.8322 (m-10) cc_final: 0.7877 (m-10) REVERT: X 117 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8208 (tppt) REVERT: Y 8 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7617 (tm-30) REVERT: Y 29 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8700 (tptm) REVERT: Z 45 MET cc_start: 0.6660 (mmm) cc_final: 0.6261 (ttm) REVERT: Z 139 MET cc_start: 0.7444 (tmm) cc_final: 0.7140 (tmm) REVERT: b 170 GLU cc_start: 0.7539 (pp20) cc_final: 0.7209 (pp20) REVERT: b 185 ASN cc_start: 0.7878 (t0) cc_final: 0.7367 (t0) outliers start: 130 outliers final: 110 residues processed: 825 average time/residue: 0.5788 time to fit residues: 783.1506 Evaluate side-chains 853 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 734 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 178 LYS Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 144 ARG Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 89 ARG Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 96 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 95 GLN Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain S residue 47 CYS Chi-restraints excluded: chain S residue 118 ASN Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 133 MET Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 75 MET Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 113 ASP Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 133 SER Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 10 ASP Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 60 GLN Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 146 TYR Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 143 LEU Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 384 optimal weight: 5.9990 chunk 515 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 446 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 134 optimal weight: 0.9990 chunk 484 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 497 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 89 optimal weight: 0.2980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.060237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.051454 restraints weight = 165037.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.053360 restraints weight = 79584.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.054653 restraints weight = 46754.373| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.8899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.340 46182 Z= 0.412 Angle : 0.795 59.198 62708 Z= 0.422 Chirality : 0.046 0.760 7346 Planarity : 0.005 0.092 7974 Dihedral : 4.636 26.486 6788 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.90 % Favored : 97.09 % Rotamer: Outliers : 2.81 % Allowed : 22.99 % Favored : 74.20 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.11), residues: 6142 helix: 0.86 (0.11), residues: 2216 sheet: -0.15 (0.13), residues: 1430 loop : -0.29 (0.13), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 215 HIS 0.009 0.001 HIS C 30 PHE 0.030 0.001 PHE K 83 TYR 0.042 0.002 TYR C 136 ARG 0.086 0.001 ARG R 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14118.63 seconds wall clock time: 252 minutes 23.61 seconds (15143.61 seconds total)